SMTL ID : 1t3q.1

Crystal structure of quinoline 2-Oxidoreductase from Pseudomonas Putida 86

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: Q.106, C.107, G.108, C.110, C.142, R.143, C.144 Chain B: M.201 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.107, A:C.110, A:C.142, A:C.144 FES.2: 12 residues within 4Å: Chain A: I.46, G.47, C.48, E.49, G.51, V.52, C.53, G.54, S.55, C.56, R.66, C.68 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.48, A:C.53, A:C.56, A:C.68 FES.15: 8 residues within 4Å: Chain D: Q.106, C.107, G.108, C.110, C.142, R.143, C.144 Chain E: M.201 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.107, D:C.110, D:C.142, D:C.144 FES.16: 12 residues within 4Å: Chain D: I.46, G.47, C.48, E.49, G.51, V.52, C.53, G.54, S.55, C.56, R.66, C.68 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.48, D:C.53, D:C.56, D:C.68

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: S.129, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.130 Water bridges: A:D.131 GOL.10: 7 residues within 4Å: Chain B: W.331, A.369, V.373, F.375, A.546, E.743 Ligands: SMO.9 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain B: R.567, Q.570, D.621 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.567 Water bridges: B:E.566, B:Q.570, B:Q.570, B:D.621 GOL.13: 6 residues within 4Å: Chain A: M.65 Chain C: G.32, T.76, N.107, R.108, T.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.107, C:R.108, C:R.108 GOL.14: 3 residues within 4Å: Chain C: L.14, V.143, R.168 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.168, C:R.168 GOL.23: 4 residues within 4Å: Chain B: W.220, R.247 Chain E: I.218, R.247 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:R.247, E:R.247, E:R.247 Water bridges: B:R.32 GOL.24: 7 residues within 4Å: Chain D: V.52, L.141 Chain E: L.708, Y.711, L.712, I.713 Chain F: R.186 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.713, F:R.186, F:R.186 GOL.25: 8 residues within 4Å: Chain E: L.692, E.694, I.696, L.712, T.774 Chain F: R.185, I.257, H.258 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:E.694, F:R.185 Water bridges: E:E.694, F:R.185, F:H.258 GOL.27: 6 residues within 4Å: Chain D: A.63, P.64, S.120 Chain F: F.78, Q.103, N.107 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:S.120, D:S.120, F:N.107 Water bridges: F:Q.103, F:N.107

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

SO4.4: 4 residues within 4Å: Chain B: S.17, P.672, M.673, E.676 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.17 Water bridges: B:S.17, B:M.673, B:E.676, B:E.676, B:R.680 SO4.5: 3 residues within 4Å: Chain B: R.168, R.318, I.358 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.168, B:R.318 SO4.6: 2 residues within 4Å: Chain B: V.165, R.168 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.168 SO4.7: 4 residues within 4Å: Chain B: P.102, N.106, R.110, T.160 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.110, B:R.110, B:R.110 Salt bridges: B:R.110 SO4.17: 4 residues within 4Å: Chain E: P.102, N.106, V.108, R.110 3 PLIP interactions: 3 interactions with chain E Water bridges: E:N.106, E:R.110 Salt bridges: E:R.110 SO4.18: 3 residues within 4Å: Chain E: R.168, R.318, I.358 3 PLIP interactions: 3 interactions with chain E Water bridges: E:L.151 Salt bridges: E:R.168, E:R.318 SO4.19: 4 residues within 4Å: Chain B: Q.215, L.243 Chain E: R.21, S.527 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.215, E:S.527 Water bridges: E:R.21 Salt bridges: E:R.21 SO4.20: 3 residues within 4Å: Chain E: P.525, A.526, S.527 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.526, E:S.527, E:S.527

2 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)

MCN.8: 34 residues within 4Å: Chain A: Q.106, C.144 Chain B: G.253, G.254, F.255, G.256, R.371, S.506, G.507, Q.508, H.510, T.513, A.544, Y.545, A.546, S.547, R.548, G.549, A.550, C.666, T.668, M.669, I.670, N.671, I.674, V.675, Q.678, I.738, K.739, G.740, M.741, G.742, E.743 Ligands: SMO.9 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.550 Hydrogen bonds: B:G.254, B:F.255, B:Q.508, B:T.513, B:Y.545, B:R.548, B:G.549, B:A.550, B:T.668, B:I.670, B:N.671, B:Q.678, B:K.739, B:M.741, B:G.742, A:Q.106 Water bridges: B:R.371, B:V.551, A:Q.106 Salt bridges: B:H.510 MCN.21: 34 residues within 4Å: Chain D: Q.106, C.144 Chain E: G.253, G.254, F.255, G.256, R.371, S.506, G.507, Q.508, H.510, T.513, A.544, Y.545, A.546, S.547, R.548, G.549, A.550, C.666, T.668, M.669, I.670, N.671, I.674, V.675, Q.678, I.738, K.739, G.740, M.741, G.742, E.743 Ligands: SMO.22 21 PLIP interactions: 19 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:A.550 Hydrogen bonds: E:G.254, E:F.255, E:Q.508, E:Y.545, E:R.548, E:G.549, E:A.550, E:T.668, E:I.670, E:N.671, E:Q.678, E:K.739, E:M.741, E:G.742, D:Q.106, D:C.107 Water bridges: E:R.371, E:R.371, E:V.551 Salt bridges: E:H.510

2 x SMO: DIOXOSULFIDOMOLYBDENUM(VI) ION(Non-covalent)

SMO.9: 10 residues within 4Å: Chain B: Q.224, F.255, G.256, Y.370, R.371, Y.545, A.546, E.743 Ligands: MCN.8, GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.224, B:A.546 SMO.22: 10 residues within 4Å: Chain E: Q.224, F.255, G.256, Y.370, R.371, V.373, Y.545, A.546, E.743 Ligands: MCN.21 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.224, E:A.546

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 33 residues within 4Å: Chain A: Q.50, G.51, V.52, L.69 Chain C: I.29, I.30, A.31, G.32, G.33, Q.34, S.35, L.36, L.53, A.73, H.77, H.99, V.100, A.101, V.105, G.109, T.110, G.113, S.114, A.116, H.117, A.122, E.123, L.160, E.164, V.165, L.166, G.188, Y.190 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.101, C:V.105, C:V.105, A:V.52, A:L.69 Hydrogen bonds: C:I.29, C:I.29, C:A.31, C:G.32, C:G.33, C:Q.34, C:S.35, C:S.35, C:L.36, C:A.101, C:T.110, C:E.123, C:E.123, C:E.123, C:L.166, C:L.166 Water bridges: C:R.28, C:A.191, C:A.191 pi-Stacking: C:Y.190 FAD.26: 33 residues within 4Å: Chain D: Q.50, G.51, V.52, L.69 Chain F: I.29, I.30, A.31, G.32, G.33, Q.34, S.35, L.36, L.53, A.73, H.77, H.99, V.100, A.101, V.105, G.109, T.110, G.113, S.114, A.116, H.117, A.122, E.123, L.160, E.164, V.165, L.166, G.188, Y.190 26 PLIP interactions: 24 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:A.101, F:V.105, F:V.105, D:V.52, D:L.69 Hydrogen bonds: F:I.29, F:I.29, F:A.31, F:G.32, F:G.33, F:Q.34, F:S.35, F:S.35, F:L.36, F:A.101, F:T.110, F:E.123, F:E.123, F:E.123, F:L.166, F:L.166 Water bridges: F:S.114, F:Y.190, F:A.191, F:A.191 pi-Stacking: F:Y.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonin, I. et al., Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase. STRUCTURE (2004)

Release Date

2004-09-14

Peptides

quinoline 2-oxidoreductase small subunit: AD
quinoline 2-oxidoreductase large subunit: BE
quinoline 2-oxidoreductase medium subunit: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

quinoline 2-oxidoreductase small subunit

quinoline 2-oxidoreductase large subunit

quinoline 2-oxidoreductase medium subunit