Difference between revisions of "Fabry:Structure-based mutation analysis"

From Bioinformatikpedia
(→‎Preparation)
(→‎Preparation)
Line 10: Line 10:
 
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Chain
  
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Chain
 
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Positions (up to 429)
  
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Positions (up to 429)
−
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDBsum
  
−
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDB
  
 
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-factor
  
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-factor
 
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-free
  
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-free
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| pH
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDBsum
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDB
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R46
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R46
Line 20: Line 21:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R46 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R46 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.262
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.262
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.301
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.301
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 8.0
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R46 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R46 [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R47
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R47
Line 30: Line 32:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R47 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R47 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.285
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.285
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.321
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.321
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 8.0
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R47 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R47 [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXN
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXN
Line 40: Line 43:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-421
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-421
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXN [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXN [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.239
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.239
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.301
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.301
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXN [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXN [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXP
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXP
Line 50: Line 54:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXP [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXP [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.204
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.204
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.265
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.265
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXP [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXP [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXT
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXT
Line 60: Line 65:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXT [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXT [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.245
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.245
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.306
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.306
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXT [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXT [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG2
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG2
Line 70: Line 76:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG2 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG2 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.202
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.202
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.6
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG2 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG2 [»]]
 
|-
 
|-
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''3HG3'''
 +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG3
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''X-ray'''
 +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''1.90'''
 +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1.90
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''A/B'''
 +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''32-426'''
 +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-426
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.167
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.197
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6.5
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG3 [»]]
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG3 [»]]
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG3 [»]]
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG3 [»]]
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''0.167'''
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| '''0.197'''
  
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG4
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG4
Line 90: Line 98:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-423
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-423
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG4 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG4 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.166
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.166
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.221
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.221
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.6
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG4 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG4 [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG5
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG5
Line 100: Line 109:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG5 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG5 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.192
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.192
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.227
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.227
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.6
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG5 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG5 [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LX9
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LX9
Line 110: Line 120:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LX9 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LX9 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.218
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.218
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LX9 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LX9 [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXA
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXA
Line 120: Line 131:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-426
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-426
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXA [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXA [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.216
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.216
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.244
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.244
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXA [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXA [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXB
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXB
Line 130: Line 142:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-427
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-427
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXB [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXB [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.227
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.227
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.264
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.264
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXB [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXB [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXC
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXC
Line 140: Line 153:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXC [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXC [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.186
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.186
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.237
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.237
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6.5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXC [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXC [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Y
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Y
Line 150: Line 164:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Y [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Y [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.195
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.195
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.230
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.230
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5.1
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Y [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Y [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Z
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Z
Line 160: Line 175:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-421
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-421
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Z [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Z [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.211
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.211
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.234
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.234
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5.1
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Z [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Z [»]]
 
|-
  
|-
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3TV8
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3TV8
Line 170: Line 186:
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-422
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3TV8 [»]]
  
−
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3TV8 [»]]
  
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.203
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.203
 
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.239
  
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.239
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4.6
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3TV8 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3TV8 [»]]
 
|-
  
|-
 
|}
  
|}

Revision as of 21:55, 20 June 2012

Preparation

<figtable id="tab:Prep"> All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3HG3 is highlighted.

Entry Method Resolution (Å) Chain Positions (up to 429) R-factor R-free pH PDBsum PDB
1R46 X-ray 3.25 A/B 32-422 0.262 0.301 8.0 [»] [»]
1R47 X-ray 3.45 A/B 32-422 0.285 0.321 8.0 [»] [»]
3GXN X-ray 3.01 A/B 32-421 0.239 0.301 4.5 [»] [»]
3GXP X-ray 2.20 A/B 32-422 0.204 0.265 4.5 [»] [»]
3GXT X-ray 2.70 A/B 32-422 0.245 0.306 4.5 [»] [»]
3HG2 X-ray 2.30 A/B 32-422 0.178 0.202 4.6 [»] [»]
3HG3 X-ray 1.90 A/B 32-426 0.167 0.197 6.5 [»] [»]
3HG4 X-ray 2.30 A/B 32-423 0.166 0.221 4.6 [»] [»]
3HG5 X-ray 2.30 A/B 32-422 0.192 0.227 4.6 [»] [»]
3LX9 X-ray 2.04 A/B 32-422 0.178 0.218 6.5 [»] [»]
3LXA X-ray 3.04 A/B 32-426 0.216 0.244 6.5 [»] [»]
3LXB X-ray 2.85 A/B 32-427 0.227 0.264 6.5 [»] [»]
3LXC X-ray 2.35 A/B 32-422 0.186 0.237 6.5 [»] [»]
3S5Y X-ray 2.10 A/B 32-422 0.195 0.230 5.1 [»] [»]
3S5Z X-ray 2.00 A/B 32-421 0.211 0.234 5.1 [»] [»]
3TV8 X-ray 2.64 A/B 32-422 0.203 0.239 4.6 [»] [»]

</figtable>

We chose to use the structure 3HG3, since it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>). The best R-factor, which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012‎) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, could be achieved with the structure 3HG4, but it has a resolution of 2.30 Å and hence we decided to use 3HG3. All structures cover the protein completely except for the signal peptide from position 1 to 31.

Vizualisation

<figure id="fig:allSNPs">

All SNPs mapped onto the structure 3HG3. Mutated sites are shown in blue. The active site (residues 170 and 231) is shown in pink, substrate binding site (position 203-207) in cyan and the existing five disulfide bonds (52 ↔ 94, 56 ↔ 63, 142 ↔ 172, 202 ↔ 223, 378 ↔ 382) are highlighted in yellow

</figure>


Create mutation

SCWRL


Comparison energies

foldX

Minimise

Gromacs

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