SMTL ID : 7e48.1

Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 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, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 3NP.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:I.21, A:D.64, A:D.64, A:V.65, A:I.95, A:G.96, A:K.165, A:I.194, A:I.194 Water bridges: A:G.14, A:A.22, A:F.41, A:I.95 pi-Stacking: A:F.41 NAD.3: 24 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 Ligands: 3NP.4 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:I.21, B:D.64, B:D.64, B:V.65, B:I.95, B:G.96, B:K.165, B:I.194, B:I.194 Water bridges: B:A.22, B:F.41, B:I.95, B:K.118 pi-Stacking: B:F.41 NAD.6: 24 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 Ligands: 3NP.7 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.21, C:F.149, C:A.191 Hydrogen bonds: C:G.14, C:I.21, C:D.64, C:V.65, C:I.95, C:G.96, C:K.165, C:I.194, C:I.194, C:T.196 Water bridges: C:A.22, C:F.41, C:F.41, C:F.41, C:I.95 pi-Stacking: C:F.41 NAD.8: 23 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, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 3NP.9 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.21, D:F.149, D:A.191 Hydrogen bonds: D:G.14, D:I.21, D:D.64, D:V.65, D:I.95, D:G.96, D:K.165, D:I.194, D:I.194, D:T.196 Water bridges: D:G.14, D:A.22, D:I.95, D:Y.158, D:L.197 pi-Stacking: D:F.41

4 x 3NP: 3-NITROPROPANOIC ACID(Non-covalent)

3NP.2: 6 residues within 4Å: Chain A: M.103, F.149, Y.158, M.161, I.202 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.158 Salt bridges: A:K.165 3NP.4: 7 residues within 4Å: Chain B: F.149, Y.158, M.161, A.198, M.199, I.202 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.158 Water bridges: B:T.196 Salt bridges: B:K.165 3NP.7: 6 residues within 4Å: Chain C: F.149, Y.158, M.161, K.165, I.202 Ligands: NAD.6 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.158 Salt bridges: C:K.165 3NP.9: 7 residues within 4Å: Chain D: F.149, Y.158, M.161, A.198, M.199, I.202 Ligands: NAD.8 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.158 Salt bridges: D:K.165

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: S.19, R.195, T.196, L.197, S.200 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.19, B:T.196, B:S.200 Water bridges: B:S.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Songsiriritthigul, C. et al., Inhibition of Mycobacterium tuberculosis InhA by 3-nitropropanoic acid. Proteins (2022)

Release Date

2021-11-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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