SMTL ID : 3of4.2 (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 FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 20 residues within 4Å: Chain A: A.13, F.65, Q.67, K.69, C.154, P.155, M.156, E.157, G.158 Chain B: A.38, S.39, S.40, Y.41, G.42, Y.114, F.115, K.118, Q.134, I.137 Ligands: GOL.12 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:P.155 Hydrogen bonds: A:Q.67, A:Q.67, A:E.157, A:G.158, B:S.39, B:S.40, B:Y.41, B:G.42, B:Y.114, B:Y.114, B:K.118, B:K.118 Water bridges: A:K.69, A:K.69, A:K.69, B:S.39, B:S.40, B:Y.41, B:Y.41 FAD.14: 20 residues within 4Å: Chain A: A.38, S.39, S.40, Y.41, G.42, Y.114, F.115, K.118, Q.134, I.137 Chain B: A.13, F.65, Q.67, K.69, C.154, P.155, M.156, E.157, G.158 Ligands: GOL.25 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:P.155 Hydrogen bonds: B:Q.67, B:Q.67, B:E.157, B:G.158, A:S.39, A:S.40, A:Y.41, A:G.42, A:Y.114, A:Y.114, A:K.118, A:K.118 Water bridges: B:K.69, B:K.69, B:K.69, A:S.39, A:S.40, A:Y.41, A:Y.41

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

SO4.2: 7 residues within 4Å: Chain A: R.11, Y.12, A.13, K.197, R.199 Chain B: A.38 Ligands: GOL.11 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.13 Water bridges: A:R.199, B:S.39, B:S.39, B:S.39 Salt bridges: A:R.11, A:K.197, A:R.199 SO4.3: 3 residues within 4Å: Chain A: F.17, S.18, G.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.17, A:G.19 SO4.4: 4 residues within 4Å: Chain A: I.159, E.160, H.161, D.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.161, A:D.162 Water bridges: A:A.163 Salt bridges: A:H.161 SO4.5: 5 residues within 4Å: Chain A: A.15, G.66, Q.67, Q.68, K.69 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.15, A:G.66, A:Q.68, A:K.69 Water bridges: A:K.69, A:K.69 Salt bridges: A:K.69 SO4.6: 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 Water bridges: A:A.87, A:R.127 SO4.7: 2 residues within 4Å: Chain A: S.123, A.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.124 Water bridges: A:A.125, A:R.127 SO4.8: 3 residues within 4Å: Chain A: H.21, T.23, D.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.24, A:D.24 Salt bridges: A:H.21 SO4.15: 7 residues within 4Å: Chain A: A.38 Chain B: R.11, Y.12, A.13, K.197, R.199 Ligands: GOL.24 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.13 Water bridges: B:R.199, A:S.39, A:S.39, A:S.39 Salt bridges: B:R.11, B:K.197, B:R.199 SO4.16: 3 residues within 4Å: Chain B: F.17, S.18, G.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.17, B:G.19 SO4.17: 4 residues within 4Å: Chain B: I.159, E.160, H.161, D.162 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.161, B:D.162 Water bridges: B:A.163 Salt bridges: B:H.161 SO4.18: 5 residues within 4Å: Chain B: A.15, G.66, Q.67, Q.68, K.69 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.15, B:G.66, B:Q.68, B:K.69 Water bridges: B:K.69, B:K.69 Salt bridges: B:K.69 SO4.19: 3 residues within 4Å: Chain B: A.85, V.86, Q.120 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.86, B:Q.120 Water bridges: B:A.87, B:R.127 SO4.20: 2 residues within 4Å: Chain B: S.123, A.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.124 Water bridges: B:A.125, B:R.127 SO4.21: 3 residues within 4Å: Chain B: H.21, T.23, D.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.24, B:D.24 Salt bridges: B:H.21

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: Q.9, W.10, R.11, Y.12, R.186, Q.193, K.197 Ligands: GOL.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.10, A:R.186, A:R.186, A:Q.193, A:K.197, A:K.197 GOL.10: 8 residues within 4Å: Chain A: K.197, V.198, R.199, Q.200 Chain B: R.35, L.36, E.96, Q.100 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.35, B:R.35, A:R.199, A:R.199 GOL.11: 7 residues within 4Å: Chain A: Y.12, T.192, Q.195, K.197 Chain B: R.101 Ligands: SO4.2, GOL.9 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.101, A:Q.195, A:K.197 Water bridges: A:T.192, A:R.199 GOL.12: 6 residues within 4Å: Chain A: E.157 Chain B: M.122, T.126, W.130, R.133 Ligands: FAD.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.133 Water bridges: B:R.133, A:E.157, A:E.157, A:E.157 GOL.13: 6 residues within 4Å: Chain A: R.133 Chain B: K.128, V.132, H.161, T.177, V.178 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.128, B:T.177, B:V.178 Water bridges: A:R.133, A:R.133 GOL.22: 8 residues within 4Å: Chain B: Q.9, W.10, R.11, Y.12, R.186, Q.193, K.197 Ligands: GOL.24 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.10, B:R.186, B:R.186, B:Q.193, B:K.197, B:K.197 GOL.23: 8 residues within 4Å: Chain A: R.35, L.36, E.96, Q.100 Chain B: K.197, V.198, R.199, Q.200 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.35, A:R.35, A:E.96, B:R.199, B:R.199 GOL.24: 7 residues within 4Å: Chain A: R.101 Chain B: Y.12, T.192, Q.195, K.197 Ligands: SO4.15, GOL.22 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.195, B:K.197, A:R.101 Water bridges: B:T.192, B:T.192, B:R.199 GOL.25: 6 residues within 4Å: Chain A: M.122, T.126, W.130, R.133 Chain B: E.157 Ligands: FAD.14 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:E.157, B:E.157, A:R.133 Hydrogen bonds: A:R.133 GOL.26: 6 residues within 4Å: Chain A: K.128, V.132, H.161, T.177, V.178 Chain B: R.133 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.128, A:T.177, A:V.178 Water bridges: A:Y.136, B:R.133, B:R.133

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
C

B
C

Nitroreductase

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