SMTL ID : 1yki.2 (1 other biounit)

The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 24 residues within 4Å: Chain A: 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 B: P.38, S.39, S.40, T.41, N.42, Q.142, L.145 Ligands: NFZ.2, CIT.3 28 PLIP interactions: 21 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.144, A:P.163, A:E.165, B:L.145 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:S.12, A:K.14, A:N.71, A:N.71, A:K.74, A:E.165, A:G.166, A:N.200, B:S.39, B:T.41 Water bridges: A:K.14, A:K.205, A:R.207, A:R.207, B:T.41, B:E.102, B:E.102, B:R.107 Salt bridges: A:R.10, A:K.205, A:R.207 FMN.6: 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: NFZ.7 29 PLIP interactions: 21 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.144, B:P.163, B:E.165, A:L.145 Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:S.12, B:K.14, B:N.71, B:N.71, B:K.74, B:E.165, B:E.165, B:G.166, B:N.200, A:S.39, A:T.41, A:N.42 Water bridges: B:K.14, B:K.205, B:R.207, A:T.41, A:R.107, A:R.121, A:R.121 Salt bridges: B:R.10, B:K.205, B:R.207

2 x NFZ: NITROFURAZONE(Non-covalent)

NFZ.2: 13 residues within 4Å: Chain A: N.67, Y.68, V.69, F.70, N.71, K.74, E.165, G.166 Chain B: S.40, T.41, F.124 Ligands: FMN.1, CIT.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.70 Hydrogen bonds: A:E.165, B:T.41 Water bridges: A:K.14, A:K.14 NFZ.7: 12 residues within 4Å: Chain A: S.40, T.41, F.124 Chain B: N.67, Y.68, V.69, F.70, N.71, K.74, E.165, G.166 Ligands: FMN.6 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.41, B:E.165, B:E.165 Hydrophobic interactions: B:F.70 Water bridges: B:K.14, B:K.14

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 6 residues within 4Å: Chain A: K.14, K.74, F.199 Chain B: N.117 Ligands: FMN.1, NFZ.2 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:K.14, B:R.107, B:R.107, B:N.117 Salt bridges: A:K.14, A:K.14, A:K.14, A:K.74

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

DMS.4: 8 residues within 4Å: Chain A: L.8, K.9, R.10, H.11, A.201, T.202, L.203, K.205 No protein-ligand interaction detected (PLIP) DMS.5: 4 residues within 4Å: Chain A: E.216, V.217 Chain B: S.52, T.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Race, P.R. et al., Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme. J.Biol.Chem. (2005)

Release Date

2005-02-08

Peptides

Oxygen-insensitive NAD(P)H nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Oxygen-insensitive NAD(P)H nitroreductase

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