Difference between revisions of "Structural Alignments (Phenylketonuria)"
From Bioinformatikpedia
(→Dataset generation) |
(→Dataset generation) |
||
| Line 8: | Line 8: | ||
Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase) |
Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase) |
||
* reference structure of PAH: 2PAH (96,41% identity) |
* reference structure of PAH: 2PAH (96,41% identity) |
||
| − | * identical sequence with filled binding site: |
+ | * identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI) |
| − | * identical sequence |
+ | * identical sequence with unfilled binding site: |
| − | * low sequence identity: 3LUY (32,2%) |
+ | * low sequence identity: 3LUY (32,2% - no pdb ID under 30%) |
* high sequence identity: pdb ID: 2PHM (89,7%) |
* high sequence identity: pdb ID: 2PHM (89,7%) |
||
* CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT |
* CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT |
||
* CA: 2B5U (CATH Code: 1.10.287.620) |
* CA: 2B5U (CATH Code: 1.10.287.620) |
||
* C: 3BQO (CATH Code: 1.25.40.210) |
* C: 3BQO (CATH Code: 1.25.40.210) |
||
| − | * other CATH category: |
+ | * other CATH category: 1V8H (CATH Code: 2.60.40.10) |
=== Pymol === |
=== Pymol === |
||
Revision as of 15:37, 28 May 2013
Contents
Summary
...
Explore structural alignments
...
Dataset generation
Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase)
- reference structure of PAH: 2PAH (96,41% identity)
- identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI)
- identical sequence with unfilled binding site:
- low sequence identity: 3LUY (32,2% - no pdb ID under 30%)
- high sequence identity: pdb ID: 2PHM (89,7%)
- CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT
- CA: 2B5U (CATH Code: 1.10.287.620)
- C: 3BQO (CATH Code: 1.25.40.210)
- other CATH category: 1V8H (CATH Code: 2.60.40.10)
Pymol
...
LGA
...
SSAP / CATHEDRAL (used by CATH)
...
Topmatch
...
SAP or CE
...
Modelling scores
...
Evaluate sequence alignments
...
References
<references/>
