SMTL ID : 3r6w.1

paAzoR1 binding to nitrofurazone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: S.10, R.12, R.15, S.16, Q.17, S.18, P.96, M.97, Y.98, N.99, F.100, S.145, R.146, G.147, G.148, F.151, E.187, E.188 Chain B: V.56, F.60 Ligands: NFZ.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.98, B:V.56, B:F.60 Hydrogen bonds: A:S.10, A:Q.17, A:S.18, A:M.97, A:M.97, A:N.99, A:F.100, A:S.145, A:G.147, A:G.148 Water bridges: A:S.10, A:R.12, A:E.187, A:E.187, A:E.188, A:E.188 Salt bridges: A:R.12 pi-Stacking: A:Y.98 FMN.10: 20 residues within 4Å: Chain A: V.56, F.60 Chain B: S.10, R.12, S.16, Q.17, S.18, P.96, M.97, Y.98, N.99, F.100, S.145, R.146, G.147, G.148, F.151, E.187 Ligands: NFZ.3, GOL.11 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.98, B:Y.98, B:Y.98, A:V.56, A:F.60 Hydrogen bonds: B:S.10, B:Q.17, B:S.18, B:M.97, B:M.97, B:N.99, B:F.100, B:S.145, B:G.147, B:G.148, B:E.187 Water bridges: B:S.10, B:R.12, B:R.12, B:R.12 Salt bridges: B:R.12 pi-Stacking: B:Y.98 FMN.13: 21 residues within 4Å: Chain C: S.10, R.12, R.15, S.16, Q.17, S.18, P.96, M.97, Y.98, N.99, F.100, S.145, R.146, G.147, G.148, F.151, E.187, E.188 Chain D: V.56, F.60 Ligands: NFZ.14 20 PLIP interactions: 2 interactions with chain D, 18 interactions with chain C Hydrophobic interactions: D:V.56, D:F.60, C:Y.98 Hydrogen bonds: C:S.10, C:Q.17, C:S.18, C:M.97, C:M.97, C:N.99, C:F.100, C:S.145, C:G.147, C:G.148 Water bridges: C:S.10, C:R.12, C:E.187, C:E.187, C:E.188 Salt bridges: C:R.12 pi-Stacking: C:Y.98 FMN.22: 20 residues within 4Å: Chain C: V.56, F.60 Chain D: S.10, R.12, S.16, Q.17, S.18, P.96, M.97, Y.98, N.99, F.100, S.145, R.146, G.147, G.148, F.151, E.187 Ligands: NFZ.15, GOL.23 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.98, D:Y.98, D:Y.98, C:V.56, C:F.60 Hydrogen bonds: D:S.10, D:Q.17, D:S.18, D:M.97, D:M.97, D:N.99, D:F.100, D:S.145, D:G.147, D:G.148, D:E.187 Water bridges: D:S.10, D:R.12, D:R.12, D:R.12 Salt bridges: D:R.12 pi-Stacking: D:Y.98

4 x NFZ: NITROFURAZONE(Non-covalent)

NFZ.2: 11 residues within 4Å: Chain A: N.99, F.100, G.148, F.151, E.188 Chain B: F.60, V.114, F.120, Y.131, F.173 Ligands: FMN.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.99, A:G.148 Water bridges: A:H.149, A:N.157 Hydrophobic interactions: B:F.173, B:F.173 NFZ.3: 10 residues within 4Å: Chain A: V.114, F.120, Y.131, F.173 Chain B: N.99, F.100, G.148, F.151, N.157 Ligands: FMN.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:V.114, B:H.149 Hydrogen bonds: B:N.157 NFZ.14: 11 residues within 4Å: Chain C: N.99, F.100, G.148, F.151, E.188 Chain D: F.60, V.114, F.120, Y.131, F.173 Ligands: FMN.13 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.99, C:G.148 Water bridges: C:H.149, C:N.157 Hydrophobic interactions: D:F.173, D:F.173 NFZ.15: 10 residues within 4Å: Chain C: V.114, F.120, Y.131, F.173 Chain D: N.99, F.100, G.148, F.151, N.157 Ligands: FMN.22 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.157 Water bridges: D:H.149, C:V.114

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.30, V.38, R.40 6 PLIP interactions: 6 interactions with chain A Water bridges: A:V.38, A:V.38, A:R.40, A:R.40 Salt bridges: A:R.30, A:R.40 SO4.16: 3 residues within 4Å: Chain C: R.30, V.38, R.40 6 PLIP interactions: 6 interactions with chain C Water bridges: C:V.38, C:V.38, C:R.40, C:R.40 Salt bridges: C:R.30, C:R.40

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: S.68, L.69, A.70 Chain C: E.14, E.23 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.68, A:A.70, C:E.14 Water bridges: A:L.69, A:L.69, C:E.14 GOL.6: 9 residues within 4Å: Chain A: P.47, L.48, A.50, S.104, G.105 Chain B: L.48, A.50, S.104, G.105 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.48, A:S.104 Water bridges: B:L.48, B:A.50 GOL.7: 5 residues within 4Å: Chain A: A.76, L.77, Q.80 Chain C: R.40, R.41 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.80, C:R.41 Water bridges: A:L.77, A:Q.80, C:R.41, C:R.41 GOL.8: 6 residues within 4Å: Chain A: R.3, L.5, A.39, G.83, E.84, D.87 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.3, A:R.3 Water bridges: A:A.39, A:A.39, A:E.84, A:E.84 GOL.9: 7 residues within 4Å: Chain A: L.90, R.139, A.140, L.141, E.178, T.180, A.212 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.139, A:E.178, A:T.180 Water bridges: A:T.180, A:L.208 GOL.11: 5 residues within 4Å: Chain A: V.56, F.60 Chain B: R.12, E.187 Ligands: FMN.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.187 Water bridges: B:R.12 GOL.12: 7 residues within 4Å: Chain B: L.69, Q.72, A.73, A.76 Chain D: R.40, R.41, E.42 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:L.69, D:E.42 Water bridges: D:R.40 GOL.17: 5 residues within 4Å: Chain A: E.14, E.23 Chain C: S.68, L.69, A.70 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:S.68, C:A.70, A:E.14, A:E.14 Water bridges: C:L.69, C:L.69, A:E.14, A:E.23 GOL.18: 9 residues within 4Å: Chain C: P.47, L.48, A.50, S.104, G.105 Chain D: L.48, A.50, S.104, G.105 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:L.48, D:A.50 Hydrogen bonds: C:L.48, C:S.104 GOL.19: 5 residues within 4Å: Chain A: R.40, R.41 Chain C: A.76, L.77, Q.80 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.41, C:Q.80 Water bridges: A:R.41, A:R.41, C:L.77, C:Q.80 GOL.20: 6 residues within 4Å: Chain C: R.3, L.5, A.39, G.83, E.84, D.87 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.3, C:R.3, C:D.87 Water bridges: C:A.39, C:A.39, C:E.84 GOL.21: 7 residues within 4Å: Chain C: L.90, R.139, A.140, L.141, E.178, T.180, A.212 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.139, C:E.178, C:E.178 Water bridges: C:T.180, C:L.208 GOL.23: 5 residues within 4Å: Chain C: V.56, F.60 Chain D: R.12, E.187 Ligands: FMN.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.187 Water bridges: D:R.12 GOL.24: 7 residues within 4Å: Chain B: R.40, R.41, E.42 Chain D: L.69, Q.72, A.73, A.76 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.42, D:L.69 Water bridges: B:R.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ryan, A. et al., Activation of nitrofurazone by azoreductases: multiple activities in one enzyme. Sci Rep (2011)

Release Date

2011-08-24

Peptides

FMN-dependent NADH-azoreductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

FMN-dependent NADH-azoreductase 1

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