SMTL ID : 1kqb.3 (2 other biounits)

Structure of Nitroreductase from E. cloacae complex with inhibitor benzoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: R.10, H.11, S.12, K.14, N.71, K.74, Y.144, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Chain B: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 Ligands: BEZ.4 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.144, A:P.163, A:E.165, A:E.165, B:L.145 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:S.12, A:K.14, A:K.14, A:N.71, A:N.71, A:E.165, A:G.166, A:N.200, B:S.39, B:T.41 Water bridges: A:R.207, B:T.41, B:R.121, B:R.121 Salt bridges: A:R.10, A:K.205, A:R.207 FMN.3: 23 residues within 4Å: Chain A: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 Chain B: R.10, H.11, S.12, K.14, N.71, K.74, Y.144, V.162, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Ligands: BEZ.2 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.144, B:P.163, A:L.145 Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:S.12, B:K.14, B:K.14, B:N.71, B:N.71, B:E.165, B:G.166, B:N.200, A:S.39, A:T.41 Water bridges: B:R.207, A:E.102 Salt bridges: B:R.10, B:K.205, B:R.207 FMN.5: 22 residues within 4Å: Chain C: R.10, H.11, S.12, K.14, N.71, K.74, Y.144, V.162, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Chain D: P.38, S.39, S.40, N.42, Q.142, L.145 Ligands: BEZ.8 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Y.144, C:P.163, C:E.165, C:E.165, D:L.145 Hydrogen bonds: C:S.12, C:S.12, C:S.12, C:S.12, C:K.14, C:K.14, C:N.71, C:N.71, C:E.165, C:G.166, C:N.200, D:S.39 Water bridges: C:K.74, C:R.207, D:T.41, D:T.41, D:E.102 Salt bridges: C:R.10, C:K.205, C:R.207 FMN.7: 23 residues within 4Å: Chain C: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 Chain D: R.10, H.11, S.12, K.14, N.71, K.74, Y.144, V.162, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Ligands: BEZ.6 24 PLIP interactions: 18 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:Y.144, D:P.163, C:L.145 Hydrogen bonds: D:S.12, D:S.12, D:S.12, D:S.12, D:K.14, D:K.14, D:N.71, D:N.71, D:K.74, D:E.165, D:G.166, D:N.200, C:S.39, C:T.41, C:N.42 Water bridges: D:R.207, C:T.41, C:R.121 Salt bridges: D:R.10, D:K.205, D:R.207

4 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 7 residues within 4Å: Chain A: S.40, T.41, F.124 Chain B: F.70, E.165, G.166 Ligands: FMN.3 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.70, B:E.165, A:T.41, A:F.124, A:F.124 Salt bridges: B:K.14 Hydrogen bonds: A:T.41 BEZ.4: 6 residues within 4Å: Chain A: E.165, G.166 Chain B: S.40, T.41, F.124 Ligands: FMN.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.165, B:T.41, B:F.124, B:F.124 Salt bridges: A:K.14 Hydrogen bonds: B:T.41 BEZ.6: 7 residues within 4Å: Chain C: S.40, T.41, F.124 Chain D: F.70, E.165, G.166 Ligands: FMN.7 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:T.41, D:F.70, D:E.165 Hydrogen bonds: C:T.41 pi-Stacking: C:F.124 Salt bridges: D:K.14 BEZ.8: 7 residues within 4Å: Chain C: F.70, E.165, G.166 Chain D: S.40, T.41, F.124 Ligands: FMN.5 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.70, C:E.165, D:T.41, D:F.124, D:F.124, D:F.124 Salt bridges: C:K.14 Hydrogen bonds: D:T.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haynes, C.A. et al., Structures of nitroreductase in three states: effects of inhibitor binding and reduction. J.Biol.Chem. (2002)

Release Date

2002-02-13

Peptides

OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE

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