SMTL ID : 3vad.1

Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 22 residues within 4Å: Chain A: N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, H.364, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.2, K.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.279, A:R.282, A:D.315, A:T.334, A:T.334, A:T.335, A:T.335, A:G.367, A:G.369, A:L.370 ADP.6: 22 residues within 4Å: Chain B: N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, H.364, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.7, K.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.279, B:R.282, B:D.315, B:T.334, B:T.335, B:T.335, B:G.367, B:G.369, B:L.370, B:T.394

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.275, N.279, G.369 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: E.275, N.279, G.369 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.328, A:D.330, A:F.333, A:G.367 K.8: 6 residues within 4Å: Chain B: V.328, D.330, F.333, G.367, P.371 Ligands: ADP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.328, B:D.330, B:F.333, B:G.367

4 x 0F1: 3,6-dichloro-1-benzothiophene-2-carboxylic acid(Non-covalent)(Covalent)

0F1.4: 12 residues within 4Å: Chain A: L.98, I.102, Y.129, L.136, V.155, L.158, L.159, H.162, R.197, F.200, R.201 Ligands: 0F1.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.102, A:L.136, A:L.158 Salt bridges: A:H.162, A:R.197 0F1.5: 11 residues within 4Å: Chain A: R.101, I.102, R.105, Y.129, A.132, L.158, H.162, S.196, R.197, F.200 Ligands: 0F1.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.102, A:R.105, A:Y.129, A:R.197, A:F.200 Salt bridges: A:H.162 pi-Stacking: A:F.200 0F1.9: 12 residues within 4Å: Chain B: L.98, I.102, Y.129, L.136, V.155, L.158, L.159, H.162, R.197, F.200, R.201 Ligands: 0F1.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.102, B:L.136, B:L.158 Salt bridges: B:H.162, B:R.197 0F1.10: 11 residues within 4Å: Chain B: R.101, I.102, R.105, Y.129, A.132, L.158, H.162, S.196, R.197, F.200 Ligands: 0F1.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.102, B:R.105, B:Y.129, B:R.197, B:F.200 Salt bridges: B:H.162 pi-Stacking: B:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmed, K. et al., Crystal structure of I170F mutant branched-chain alpha-ketoacid dehydrogenase kinase in complex with 3,6-dichlorobenzo[b]thiophene-2-carboxylic acid. To be Published

Release Date

2013-01-16

Peptides

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial