SMTL ID : 7kxa.1

Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.22, I.23, I.24, S.28, I.29, F.49, L.71, D.72, V.73, S.102, I.103, G.104, I.130, M.155, D.156, F.157, M.169, K.173, A.199, G.200, P.201, I.202, T.204, M.207 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.157, A:F.157, A:A.199 Hydrogen bonds: A:G.22, A:S.28, A:I.29, A:D.72, A:V.73, A:I.103, A:G.104, A:K.173, A:I.202, A:I.202, A:T.204 Water bridges: A:A.30, A:F.49, A:F.49, A:F.49, A:I.103, A:G.104, A:L.205 pi-Stacking: A:F.49 NAD.5: 24 residues within 4Å: Chain B: G.22, I.23, I.24, S.28, I.29, F.49, L.71, D.72, V.73, S.102, I.103, G.104, I.130, M.155, D.156, F.157, M.169, K.173, A.199, G.200, P.201, I.202, T.204, M.207 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.157, B:F.157, B:A.199 Hydrogen bonds: B:G.22, B:S.28, B:I.29, B:D.72, B:V.73, B:I.103, B:G.104, B:K.173, B:I.202, B:I.202, B:T.204 Water bridges: B:A.30, B:F.49, B:F.49, B:F.49, B:I.103, B:G.104, B:L.205 pi-Stacking: B:F.49 NAD.9: 24 residues within 4Å: Chain C: G.22, I.23, I.24, S.28, I.29, F.49, L.71, D.72, V.73, S.102, I.103, G.104, I.130, M.155, D.156, F.157, M.169, K.173, A.199, G.200, P.201, I.202, T.204, M.207 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:F.157, C:F.157, C:A.199 Hydrogen bonds: C:G.22, C:S.28, C:I.29, C:D.72, C:D.72, C:V.73, C:I.103, C:G.104, C:K.173, C:I.202, C:I.202 Water bridges: C:A.30, C:F.49, C:F.49, C:F.49, C:I.103, C:G.104, C:L.205 pi-Stacking: C:F.49 NAD.13: 24 residues within 4Å: Chain D: G.22, I.23, I.24, S.28, I.29, F.49, L.71, D.72, V.73, S.102, I.103, G.104, I.130, M.155, D.156, F.157, M.169, K.173, A.199, G.200, P.201, I.202, T.204, M.207 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:F.157, D:F.157, D:A.199 Hydrogen bonds: D:G.22, D:S.28, D:I.29, D:D.72, D:D.72, D:V.73, D:I.103, D:G.104, D:K.173, D:I.202, D:I.202 Water bridges: D:A.30, D:F.49, D:F.49, D:F.49, D:I.103, D:G.104, D:L.205 pi-Stacking: D:F.49

4 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: D.231, Q.232, A.234 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.231, A:Q.232, A:A.234, H2O.9, H2O.9 K.6: 3 residues within 4Å: Chain B: D.231, Q.232, A.234 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.231, B:Q.232, B:A.234, H2O.19, H2O.19 K.10: 3 residues within 4Å: Chain C: D.231, Q.232, A.234 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.231, C:Q.232, C:A.234, H2O.29, H2O.30 K.14: 3 residues within 4Å: Chain D: D.231, Q.232, A.234 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.231, D:Q.232, D:A.234, H2O.39, H2O.40

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: E.70, E.77, H.78, T.81, R.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.70, A:T.81 EDO.7: 5 residues within 4Å: Chain B: E.70, E.77, H.78, T.81, R.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.70, B:T.81 EDO.11: 5 residues within 4Å: Chain C: E.70, E.77, H.78, T.81, R.85 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.70, C:E.70, C:T.81, C:T.81 EDO.15: 5 residues within 4Å: Chain D: E.70, E.77, H.78, T.81, R.85 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.70, D:E.70, D:T.81, D:T.81

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 6 residues within 4Å: Chain A: F.117, D.118, A.119, P.120 Chain C: Y.133, K.140 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Water bridges: A:F.117, C:Y.133 Hydrogen bonds: C:Y.133, C:Y.133 Salt bridges: C:K.140 PO4.8: 6 residues within 4Å: Chain B: F.117, D.118, A.119, P.120 Chain D: Y.133, K.140 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Water bridges: B:F.117, D:Y.133 Hydrogen bonds: D:Y.133, D:Y.133 Salt bridges: D:K.140 PO4.12: 6 residues within 4Å: Chain A: Y.133, K.140 Chain C: F.117, D.118, A.119, P.120 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Water bridges: C:F.117, A:Y.133 Hydrogen bonds: A:Y.133 Salt bridges: A:K.140 PO4.16: 6 residues within 4Å: Chain B: Y.133, K.140 Chain D: F.117, D.118, A.119, P.120 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.133 Water bridges: B:Y.133, D:F.117 Salt bridges: B:K.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii in complex with NAD. to be published

Release Date

2020-12-16

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Enoyl-[acyl-carrier-protein] reductase [NADH]

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