SMTL ID : 7nnx.1

E. coli NfsA with 1,4-benzoquinone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x HQE: benzene-1,4-diol(Covalent)

HQE.1: 5 residues within 4Å: Chain A: C.90, P.91, D.92 Chain B: R.217, I.221 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.217, B:I.221 pi-Cation interactions: B:R.217 Hydrogen bonds: A:D.92 HQE.9: 5 residues within 4Å: Chain A: R.217, I.221 Chain B: C.90, P.91, D.92 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.217, A:I.221 pi-Cation interactions: A:R.217 Hydrogen bonds: B:D.92

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: S.38, S.39, S.40, F.42, V.106, D.107, M.110 Chain B: H.11, R.12, S.13, R.15, Q.67, V.127, Y.128, I.129, G.130, G.131, K.167, R.169 Ligands: PLQ.8 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.128, B:Y.128, A:V.106 Hydrogen bonds: B:S.13, B:S.13, B:R.15, B:Q.67, B:Q.67, B:G.130, B:G.131, B:K.167, A:S.38, A:S.38, A:S.39 Water bridges: B:H.11, B:R.15, B:R.15, B:K.167, B:R.169, A:S.38 Salt bridges: B:H.11, B:R.169 FMN.10: 20 residues within 4Å: Chain A: H.11, R.12, S.13, R.15, Q.67, V.127, Y.128, I.129, G.130, G.131, K.167, R.169 Chain B: S.38, S.39, S.40, F.42, V.106, D.107, M.110 Ligands: PLQ.16 22 PLIP interactions: 5 interactions with chain B, 17 interactions with chain A Hydrophobic interactions: B:V.106, A:Y.128, A:Y.128 Hydrogen bonds: B:S.38, B:S.38, B:S.39, A:S.13, A:S.13, A:R.15, A:Q.67, A:Q.67, A:G.130, A:G.131, A:K.167 Water bridges: B:S.38, A:H.11, A:R.15, A:R.15, A:K.167, A:R.169 Salt bridges: A:H.11, A:R.169

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

DMS.3: 5 residues within 4Å: Chain A: N.134, N.135, I.136, E.137, F.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.137 Water bridges: A:A.138 pi-Cation interactions: A:F.227 DMS.11: 5 residues within 4Å: Chain B: N.134, N.135, I.136, E.137, F.227 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.137 Water bridges: B:A.138 pi-Cation interactions: B:F.227

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: T.2, P.3, T.4 Chain B: S.121 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.121 Hydrogen bonds: A:T.4, A:T.4 EDO.5: 5 residues within 4Å: Chain A: C.9, R.169 Chain B: N.32, R.35, A.36 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.169, A:R.169 EDO.7: 2 residues within 4Å: Chain A: E.20, W.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.20 EDO.12: 4 residues within 4Å: Chain A: S.121 Chain B: T.2, P.3, T.4 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.2, B:T.4, B:T.4, B:T.4 Water bridges: A:S.121 EDO.13: 5 residues within 4Å: Chain A: N.32, R.35, A.36 Chain B: C.9, R.169 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.169, B:R.169 EDO.15: 2 residues within 4Å: Chain B: E.20, W.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.20 Water bridges: B:E.20

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain B: G.130, R.225 Ligands: PLQ.8 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: G.130, R.225 Ligands: PLQ.16 Ligand excluded by PLIP

2 x PLQ: 1,4-benzoquinone(Non-covalent)

PLQ.8: 5 residues within 4Å: Chain A: S.40, S.41 Chain B: Q.67 Ligands: FMN.2, CL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.41 PLQ.16: 5 residues within 4Å: Chain A: Q.67 Chain B: S.40, S.41 Ligands: FMN.10, CL.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Day, M.A. et al., The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN. Biochem.J. (2021)

Release Date

2021-07-21

Peptides

Oxygen-insensitive NADPH nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Oxygen-insensitive NADPH nitroreductase

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