SMTL ID : 2wzw.1

Crystal structure of the FMN-dependent nitroreductase NfnB from Mycobacterium smegmatis in complex with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: R.26, R.27, A.28, R.30, F.109, Y.130, Y.138, P.180, Q.181, A.182, L.183, I.222, R.224 Chain B: P.53, S.54, N.55, S.56, N.57, D.159, I.162 Ligands: NDP.2, PO4.6 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.180, A:A.182, B:I.162 Hydrogen bonds: A:A.28, A:R.30, A:Y.138, A:A.182, A:L.183, B:S.54, B:S.56 Water bridges: A:R.26, A:A.28, A:R.30, A:S.134, A:Y.138, A:Y.138, A:Y.138, A:Q.181, A:I.222, A:I.222 Salt bridges: A:R.26, A:R.224 FMN.5: 21 residues within 4Å: Chain A: P.53, S.54, N.55, S.56, N.57, D.159, I.162 Chain B: R.26, R.27, A.28, R.30, F.109, Y.130, Y.138, P.180, Q.181, A.182, L.183, I.222, R.224 Ligands: PO4.3 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.180, A:I.162 Hydrogen bonds: B:A.28, B:R.30, B:Y.138, B:A.182, B:L.183, A:S.54, A:S.56 Water bridges: B:A.28, B:R.30, B:R.30, B:S.134, B:Y.138, B:Q.181, B:I.222, B:R.224, B:R.224 Salt bridges: B:R.26, B:R.224

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 14 residues within 4Å: Chain A: Y.93, R.106, A.107, G.110, S.111, Y.114, I.119, A.120, R.121, L.183, F.186 Chain B: S.56 Ligands: FMN.1, PO4.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.93 Hydrogen bonds: A:R.106, A:I.119, A:N.131 Water bridges: A:Y.93, A:R.106, A:R.106, A:R.121, A:R.121, A:R.121, A:R.121, A:N.131 Salt bridges: A:R.106, A:R.106 pi-Stacking: A:Y.114, A:F.186

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: N.55, S.56 Chain B: F.109 Ligands: FMN.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.56 Water bridges: A:S.56 PO4.4: 3 residues within 4Å: Chain A: H.62, E.64 Chain B: R.232 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:H.62, A:R.200 Salt bridges: A:H.62, B:R.232 PO4.6: 5 residues within 4Å: Chain A: F.109 Chain B: N.55, S.56 Ligands: FMN.1, NDP.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.56 Water bridges: A:Y.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manina, G. et al., Biological and Structural Characterization of the Mycobacterium Smegmatis Nitroreductase Nfnb, and its Role in Benzothiazinone Resistance. Mol.Microbiol. (2010)

Release Date

2010-07-14

Peptides

NFNB PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NFNB PROTEIN

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