Structure-based mutation analysis BCKDHA

Structure selection

The following table presents the PDB structures for BCKDHA to date:

PDB id	resolution [Å]	R-factor	coverage	ph-value
1DTW	2.70	0.224		7.5*
1OLS	1.85	0.172		5.5
1OLU	1.90	0.161		5.5
1OLX	2.25	0.161		5.5
1U5B	1.83	0.156		5.8
1V11	1.95	0.139*		5.5
1V16	1.90	0.132*		5.5
1V1M	2.00	0.130*		5.5
1V1R	1.80	0.158		5.5
1WCI	1.84	0.149		5.5
1X7W	1.73	0.148		5.8
1X7X	2.10	0.149		5.8
1X7Y	1.57	0.150		5.8
1X7Z	1.72	0.154		5.8
1X80	2.00	0.161		5.8
2BEU	1.89	0.171		5.5
2BEV	1.80	0.139		5.5
2BEW	1.79	0.147		5.5
2BFB	1.77	0.145		5.5
2BFC	1.64	0.144		5.5
2BFD	1.39*	0.150		5.5
2BFE	1.69	0.150		5.5
2BFF	1.46	0.150		5.5
2J9F	1.88	0.171		5.5

The following PDB Structure was chosen because of its good experimental resolution: <bold></bold>

• resultion:
• R-factor
• ph-value

Mapping of the mutations on thw crystal structure

SCWRL

Before we could use SCWRL we first had to get the sequence of our model: repairPDB bckdha.pdb -seq >> bckdha.seq

When we have the sequence we have to make one file for each mutation. In these files we copied the bckdha.seq and changed the sequence to lower case letters. Then we add the mutation in an upper case letter.

To run SCWRL we used the command: scwrl -i bckdha.pdb -s mutation1.seq -o mutation1Model.pdb

Gromacs

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