SMTL ID : 4tro.1

Structure of the enoyl-ACP reductase of Mycobacterium tuberculosis InhA, inhibited with the active metabolite of isoniazid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: ZID.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.21, A:F.149, A:A.191 Hydrogen bonds: A:G.14, A:S.20, A:I.21, A:D.64, A:D.64, A:V.65, A:G.96, A:K.165, A:G.192, A:I.194 Water bridges: A:G.14, A:A.22, A:F.41, A:I.95, A:G.96 NAD.11: 25 residues within 4Å: Chain B: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: ZID.12 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.21, B:F.149, B:A.191 Hydrogen bonds: B:G.14, B:S.20, B:I.21, B:D.64, B:D.64, B:V.65, B:G.96, B:K.165, B:G.192, B:I.194 Water bridges: B:G.14, B:A.22, B:F.41, B:I.95, B:G.96 NAD.21: 25 residues within 4Å: Chain C: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: ZID.22 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.21, C:F.149, C:A.191 Hydrogen bonds: C:G.14, C:S.20, C:I.21, C:D.64, C:V.65, C:G.96, C:K.165, C:G.192, C:I.194, C:T.196 Water bridges: C:G.14, C:A.22, C:F.41, C:I.95, C:G.96 NAD.31: 25 residues within 4Å: Chain D: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: ZID.32 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.21, D:F.149, D:A.191 Hydrogen bonds: D:G.14, D:S.20, D:I.21, D:D.64, D:V.65, D:G.96, D:K.165, D:G.192, D:I.194, D:T.196 Water bridges: D:G.14, D:A.22, D:F.41, D:I.95, D:G.96

4 x ZID: ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE(Covalent)

ZID.2: 27 residues within 4Å: Chain A: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, Y.158, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199, W.222 Ligands: NAD.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.149, A:F.149, A:F.149, A:Y.158 Hydrogen bonds: A:G.14, A:S.20, A:I.21, A:D.64, A:V.65, A:G.96, A:K.165, A:I.194 Water bridges: A:A.22, A:F.41, A:F.41, A:F.41, A:D.64, A:I.95, A:T.196, A:T.196 pi-Stacking: A:F.41 ZID.12: 27 residues within 4Å: Chain B: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, Y.158, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199, W.222 Ligands: NAD.11 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.149, B:F.149, B:F.149, B:Y.158 Hydrogen bonds: B:G.14, B:S.20, B:I.21, B:D.64, B:V.65, B:G.96, B:K.165, B:I.194 Water bridges: B:A.22, B:F.41, B:F.41, B:F.41, B:D.64, B:I.95, B:T.196, B:T.196 pi-Stacking: B:F.41 ZID.22: 27 residues within 4Å: Chain C: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, Y.158, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199, W.222 Ligands: NAD.21 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:F.149, C:F.149, C:F.149, C:Y.158 Hydrogen bonds: C:G.14, C:S.20, C:I.21, C:V.65, C:G.96, C:K.165, C:I.194 Water bridges: C:A.22, C:F.41, C:F.41, C:F.41, C:D.64, C:I.95, C:Y.158, C:T.196, C:T.196, C:L.197 pi-Stacking: C:F.41 ZID.32: 27 residues within 4Å: Chain D: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, Y.158, M.161, K.165, A.191, G.192, P.193, I.194, T.196, M.199, W.222 Ligands: NAD.31 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:F.149, D:F.149, D:F.149, D:Y.158 Hydrogen bonds: D:G.14, D:S.20, D:I.21, D:V.65, D:G.96, D:K.165, D:I.194 Water bridges: D:A.22, D:F.41, D:F.41, D:F.41, D:D.64, D:I.95, D:Y.158, D:T.196, D:T.196, D:L.197 pi-Stacking: D:F.41

8 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 6 residues within 4Å: Chain A: D.42, R.43, L.44, R.45, E.62, H.70 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.42, A:L.44, A:R.45 Water bridges: A:L.46 Salt bridges: A:R.45, A:E.62, A:E.62 EPE.4: 10 residues within 4Å: Chain A: S.19, H.24, I.194, R.195, T.196, M.232, K.233, D.234, A.235, T.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:K.233, A:A.235 Salt bridges: A:H.24 EPE.13: 6 residues within 4Å: Chain B: D.42, R.43, L.44, R.45, E.62, H.70 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.42, B:L.44, B:R.45 Water bridges: B:L.46 Salt bridges: B:R.45, B:E.62, B:E.62 EPE.14: 10 residues within 4Å: Chain B: S.19, H.24, I.194, R.195, T.196, M.232, K.233, D.234, A.235, T.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.195, B:K.233, B:A.235 Salt bridges: B:H.24 EPE.23: 6 residues within 4Å: Chain C: D.42, R.43, L.44, R.45, E.62, H.70 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.42, C:L.44, C:R.45 Water bridges: C:L.46, C:E.62 Salt bridges: C:R.45, C:E.62, C:E.62 EPE.24: 10 residues within 4Å: Chain C: S.19, H.24, I.194, R.195, T.196, M.232, K.233, D.234, A.235, T.236 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.195, C:K.233, C:A.235 Salt bridges: C:H.24 EPE.33: 6 residues within 4Å: Chain D: D.42, R.43, L.44, R.45, E.62, H.70 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.42, D:L.44, D:R.45 Water bridges: D:L.46, D:E.62 Salt bridges: D:R.45, D:E.62, D:E.62 EPE.34: 10 residues within 4Å: Chain D: S.19, H.24, I.194, R.195, T.196, M.232, K.233, D.234, A.235, T.236 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.195, D:K.233, D:A.235 Salt bridges: D:H.24

16 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: I.228, G.229, W.230, N.231 Ligand excluded by PLIP DMS.6: 6 residues within 4Å: Chain A: I.228 Chain D: G.141, G.142, G.183, R.185, P.251 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: K.132, P.136, Y.182 Chain C: F.109 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: E.68, Y.125, K.132 Chain C: D.110 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain B: I.228, G.229, W.230, N.231 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain B: I.228 Chain C: G.141, G.142, G.183, R.185, P.251 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain B: K.132, P.136, Y.182 Chain D: F.109 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain B: E.68, Y.125, K.132 Chain D: D.110 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain C: I.228, G.229, W.230, N.231 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain B: G.141, G.142, G.183, R.185, P.251 Chain C: I.228 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: F.109 Chain C: K.132, P.136, Y.182 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: D.110 Chain C: E.68, Y.125, K.132 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain D: I.228, G.229, W.230, N.231 Ligand excluded by PLIP DMS.36: 6 residues within 4Å: Chain A: G.141, G.142, G.183, R.185, P.251 Chain D: I.228 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain B: F.109 Chain D: K.132, P.136, Y.182 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: D.110 Chain D: E.68, Y.125, K.132 Ligand excluded by PLIP

8 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: D.223, Q.224, A.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.224 NA.10: 3 residues within 4Å: Chain A: G.141, R.185, D.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.8, A:G.141, A:R.185, A:D.248 NA.19: 3 residues within 4Å: Chain B: D.223, Q.224, A.226 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.224 NA.20: 3 residues within 4Å: Chain B: G.141, R.185, D.248 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.8, B:K.8, B:R.185, B:D.248 NA.29: 3 residues within 4Å: Chain C: D.223, Q.224, A.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.223 NA.30: 3 residues within 4Å: Chain C: G.141, R.185, D.248 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.8, C:R.185, C:D.248 NA.39: 3 residues within 4Å: Chain D: D.223, Q.224, A.226 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.224 NA.40: 3 residues within 4Å: Chain D: G.141, R.185, D.248 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.8, D:G.141, D:R.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chollet, A. et al., Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach. J.Struct.Biol. (2015)

Release Date

2015-04-29

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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