SMTL ID : 6lky.1

Crystal structure of isocitrate dehydrogenase from Methylococcus capsulatus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: I.12, K.66, P.68, L.69, T.70, T.71, N.81, L.244, G.245, E.260, A.261, V.262, H.263, G.264, S.265, A.266, P.267, D.268, I.269, A.275, N.276 Chain B: N.176, I.205, A.208, M.211 Ligands: ACE.2, CIT.3 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.66, A:L.69, A:L.69, A:T.71, A:T.71, A:N.81, A:H.263, A:G.264, A:S.265, A:A.266, A:D.268, A:N.276, B:N.176 Water bridges: A:E.260, A:E.260, A:A.279, A:D.317 pi-Stacking: A:H.263, A:H.263 NAD.6: 27 residues within 4Å: Chain A: N.176, I.205, A.208, M.211 Chain B: I.12, K.66, P.68, L.69, T.70, T.71, N.81, R.85, L.244, G.245, E.260, V.262, H.263, G.264, S.265, A.266, P.267, D.268, I.269, A.275, N.276, D.317 Ligands: CIT.11 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.66, B:L.69, B:T.71, B:T.71, B:T.71, B:N.81, B:N.81, B:R.85, B:H.263, B:G.264, B:S.265, B:A.266, B:D.268, B:N.276, A:N.176 Water bridges: B:L.244, B:A.279 pi-Stacking: B:H.263

5 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.2: 6 residues within 4Å: Chain A: G.243, L.244, G.245 Chain B: M.211, M.215 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.244, A:G.245 ACE.5: 2 residues within 4Å: Chain A: V.214 Chain B: A.106 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.106 ACE.7: 8 residues within 4Å: Chain A: I.177, L.178 Chain B: L.122, A.124, G.125, I.126, E.127, I.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.124, B:G.125, B:I.126, B:I.142 ACE.8: 2 residues within 4Å: Chain B: G.102, E.309 No protein-ligand interaction detected (PLIP) ACE.9: 5 residues within 4Å: Chain B: P.49, R.78, S.79, V.80, T.83 No protein-ligand interaction detected (PLIP)

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 13 residues within 4Å: Chain A: T.71, S.79, N.81, R.85, R.95, R.116, Y.123, D.231 Chain B: K.174, N.176, I.177, D.207 Ligands: NAD.1 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:T.71, A:N.81, A:Y.123, B:K.174, B:N.176, B:D.207 Salt bridges: A:R.85, A:R.85, A:R.95, A:R.116, A:R.116, B:K.174 Hydrophobic interactions: B:I.177 Water bridges: B:K.174 CIT.11: 13 residues within 4Å: Chain A: K.174, N.176, I.177, D.207 Chain B: T.71, S.79, N.81, R.85, R.95, R.116, Y.123, D.231 Ligands: NAD.6 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.123, A:I.177 Hydrogen bonds: B:T.71, B:S.79, B:S.79, B:N.81, A:K.174, A:N.176, A:D.207, A:D.207 Water bridges: B:R.95, B:D.231 Salt bridges: B:R.85, B:R.85, B:R.95, B:R.116, B:R.116, A:K.174

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 7 residues within 4Å: Chain A: K.168, T.170, D.202, R.204, Q.212, R.219, F.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.168 Salt bridges: A:K.168, A:R.204 ACT.10: 3 residues within 4Å: Chain B: F.129, I.130, K.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G.P., Crystal structure of isocitrate dehydrogenase from Methylococcus capsulatus. To Be Published

Release Date

2020-12-23

Peptides

Putative isocitrate dehydrogenase, NAD-dependent: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative isocitrate dehydrogenase, NAD-dependent