SMTL ID : 4bii.1

How nature bridges the gap: Crystallographic elucidation of pyridomycin binding to InhA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

3 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: PYW.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: 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:I.95, A:G.96, A:K.165, A:I.194, A:T.196, A:T.196, A:T.196 Water bridges: A:A.22, A:F.41, 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, F.97, I.122, M.147, D.148, F.149, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: PYW.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.149, B:A.191 Hydrogen bonds: B:G.14, B:S.20, B:I.21, B:D.64, B:V.65, B:I.95, B:G.96, B:K.165, B:I.194, B:T.196, B:T.196 Water bridges: B:A.22, B:I.95 pi-Stacking: B:F.41 NAD.5: 21 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, K.165, A.191, G.192, P.193, I.194 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.21, C:F.149, C:F.149, C:A.191 Hydrogen bonds: C:G.14, C:I.21, C:D.64, C:D.64, C:V.65, C:I.95, C:G.96, C:K.165, C:I.194, C:I.194 Water bridges: C:S.19, C:A.22, C:F.41, C:F.41, C:I.95, C:I.194 pi-Stacking: C:F.41

3 x PYW: PYRIDOMYCIN(Covalent)(Non-covalent)

PYW.2: 16 residues within 4Å: Chain A: I.21, S.94, I.95, G.96, M.103, M.147, D.148, F.149, A.157, Y.158, M.161, K.165, G.192, P.193, I.194 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.21, A:M.147, A:A.157, A:Y.158, A:Y.158 Hydrogen bonds: A:K.165, A:I.194, A:I.194 Water bridges: A:I.21 PYW.4: 16 residues within 4Å: Chain B: I.21, S.94, I.95, G.96, M.103, M.147, D.148, F.149, A.157, Y.158, M.161, K.165, G.192, P.193, I.194 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.21, B:M.147, B:A.157, B:Y.158, B:Y.158, B:Y.158 Hydrogen bonds: B:K.165, B:I.194, B:I.194 PYW.6: 15 residues within 4Å: Chain D: S.94, I.95, G.96, M.103, M.147, D.148, F.149, A.157, Y.158, M.161, K.165, G.192, P.193, I.194, M.199 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:M.147, D:F.149, D:F.149, D:A.157 Hydrogen bonds: D:K.165, D:I.194, D:I.194 Water bridges: D:G.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hartkoorn, R. et al., Pyridomycin Bridges the Nadh and Substrate Binding Pockets of the Enoyl Reductase Inha. Nat.Chem.Biol. (2014)

Release Date

2013-12-04

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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