SMTL ID : 3of4.1 (1 other biounit)

Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 22 residues within 4Å: Chain A: R.11, Y.12, A.13, Q.67, K.69, Y.136, C.154, P.155, M.156, E.157, G.158, K.197, R.199 Chain B: A.38, S.39, S.40, Y.41, G.42, Q.134, I.137 Ligands: GOL.11, UNL.14 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.136, A:P.155, A:P.155 Hydrogen bonds: A:A.13, A:Q.67, A:Q.67, A:K.69, A:E.157, A:G.158, B:Y.41 Water bridges: A:R.199 Salt bridges: A:R.11, A:K.197, A:R.199 FMN.15: 22 residues within 4Å: Chain A: A.38, S.39, S.40, Y.41, G.42, Q.134, I.137 Chain B: R.11, Y.12, A.13, Q.67, K.69, Y.136, C.154, P.155, M.156, E.157, G.158, K.197, R.199 Ligands: UNL.2, GOL.7 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.136, B:P.155 Hydrogen bonds: B:A.13, B:Q.67, B:Q.67, B:K.69, B:E.157, B:G.158, A:Y.41 Water bridges: B:K.197, B:K.197, B:R.199 Salt bridges: B:R.11, B:K.197, B:R.199

2 x UNL: UNKNOWN LIGAND

UNL.2: 8 residues within 4Å: Chain A: S.40, Y.41, Y.114 Chain B: F.65, Q.67, G.158 Ligands: GOL.7, FMN.15 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.65, B:Q.67, B:Q.67, B:Q.67, A:Y.41, A:Y.114, A:K.118 UNL.14: 6 residues within 4Å: Chain A: F.65, Q.67, G.158 Chain B: S.40, Y.41 Ligands: FMN.1 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.65, A:Q.67, A:Q.67, A:Q.67, B:Y.41, B:Y.41 Water bridges: B:Y.41

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

SO4.3: 4 residues within 4Å: Chain A: I.159, E.160, H.161, D.162 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.161, A:D.162, A:D.162 Water bridges: A:I.159, A:A.163, A:A.163 Salt bridges: A:H.161 SO4.4: 4 residues within 4Å: Chain A: H.21, I.22, T.23, D.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.24 Salt bridges: A:H.21 SO4.5: 3 residues within 4Å: Chain A: A.85, V.86, Q.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.86, A:Q.120, A:Q.120 Water bridges: A:A.87 SO4.6: 4 residues within 4Å: Chain A: I.51, R.52, N.53 Chain B: L.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.52, A:N.53 SO4.16: 4 residues within 4Å: Chain B: I.159, E.160, H.161, D.162 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.161, B:D.162 Salt bridges: B:H.161 SO4.17: 2 residues within 4Å: Chain B: S.123, A.124 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.124 Water bridges: B:A.125, B:A.125, B:A.125, B:R.127 SO4.18: 5 residues within 4Å: Chain B: A.15, G.66, Q.67, Q.68, K.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.68, B:K.69 Water bridges: B:K.69, B:K.69 Salt bridges: B:K.69

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: R.101 Chain B: Q.195 Ligands: UNL.2, FMN.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.101, A:R.101 Water bridges: A:Y.93 GOL.8: 3 residues within 4Å: Chain A: T.104, N.105, E.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.105, A:E.106 GOL.9: 8 residues within 4Å: Chain A: R.35, L.36, E.96, Q.100 Chain B: Q.9, K.197, V.198, R.199 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.9, B:Q.9, B:R.199, B:R.199, A:R.35, A:R.35 GOL.10: 8 residues within 4Å: Chain A: Q.9, W.10, R.11, Y.12, R.186, Q.193, K.197 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.10, A:R.186, A:R.186, A:K.197, A:K.197 GOL.11: 7 residues within 4Å: Chain A: Y.12, T.192, Q.195, K.197 Chain B: R.101 Ligands: FMN.1, GOL.10 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.195, A:K.197, A:K.197, B:R.101 Water bridges: A:R.199 GOL.12: 1 residues within 4Å: Chain A: Y.185 No protein-ligand interaction detected (PLIP) GOL.13: 5 residues within 4Å: Chain A: Q.9, K.197, R.199 Chain B: R.35, L.36 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.9, A:K.197, A:R.199, B:R.35 Water bridges: A:R.199, B:R.35 GOL.20: 5 residues within 4Å: Chain B: L.7, W.10, A.147, E.148, E.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.147 GOL.21: 7 residues within 4Å: Chain B: Q.9, W.10, R.11, Y.12, R.186, Q.193, K.197 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.186, B:R.186, B:Q.193, B:K.197, B:K.197 GOL.22: 3 residues within 4Å: Chain B: S.18, S.187, E.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.188, B:E.188 Water bridges: B:G.19 GOL.23: 3 residues within 4Å: Chain B: Q.59, N.62, H.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.59, B:N.62

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.19: 3 residues within 4Å: Chain B: A.85, V.86, Q.120 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.86, B:Q.120 Water bridges: B:A.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution. To be published

Release Date

2010-08-25

Peptides

Nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitroreductase

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