SMTL ID : 3nvy.1

Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.111, C.112, G.113, C.115, C.147, R.148, C.149 Chain C: L.174 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.112, A:C.115, A:C.147, A:C.149 FES.2: 10 residues within 4Å: Chain A: G.41, C.42, G.43, G.45, G.46, C.47, G.48, C.50, N.70, C.72 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.42, A:C.47, A:C.50, A:C.72 FES.7: 9 residues within 4Å: Chain D: Q.111, C.112, G.113, C.115, C.147, R.148, C.149, T.150 Chain F: L.174 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.112, D:C.115, D:C.147, D:C.149 FES.8: 10 residues within 4Å: Chain D: G.41, C.42, G.43, G.45, G.46, C.47, G.48, C.50, N.70, C.72 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.42, D:C.47, D:C.50, D:C.72

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

FAD.3: 27 residues within 4Å: Chain A: E.44, G.45 Chain B: K.62, L.63, V.64, V.65, G.66, N.67, T.68, E.69, I.70, A.107, L.111, F.143, A.144, V.148, V.151, A.152, S.153, G.156, N.157, I.159, T.160, S.165, D.166, I.209, L.210 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.144, B:V.148, B:V.148 Hydrogen bonds: B:L.63, B:L.63, B:V.65, B:G.66, B:N.67, B:T.68, B:E.69, B:I.70, B:S.153, B:D.166, B:D.166, B:D.166, B:L.210, B:L.210 Water bridges: B:A.144, B:A.144, B:K.239 pi-Stacking: B:F.143 FAD.9: 26 residues within 4Å: Chain D: E.44, G.45 Chain E: K.62, L.63, V.64, V.65, G.66, N.67, T.68, E.69, I.70, A.107, L.111, F.143, A.144, V.148, A.152, S.153, G.156, N.157, I.159, T.160, S.165, D.166, I.209, L.210 25 PLIP interactions: 25 interactions with chain E Hydrophobic interactions: E:A.144, E:V.148 Hydrogen bonds: E:K.62, E:L.63, E:V.65, E:G.66, E:N.67, E:T.68, E:T.68, E:E.69, E:E.69, E:E.69, E:I.70, E:S.153, E:N.157, E:N.157, E:T.160, E:D.166, E:D.166, E:L.210, E:L.210 Water bridges: E:A.144, E:A.144, E:S.153 pi-Stacking: E:F.143

2 x MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER(Non-covalent)

MTE.4: 19 residues within 4Å: Chain A: Q.111, C.149 Chain C: G.226, G.227, F.228, G.229, R.342, M.468, G.469, Q.470, A.508, A.509, S.510, V.511, S.512, Q.624, G.690, E.691 Ligands: MOS.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.227, C:F.228, C:M.468, C:Q.470, C:S.510, C:S.512, C:S.512, C:Q.624, C:Q.624, A:Q.111 Water bridges: C:R.342, C:G.690 MTE.10: 19 residues within 4Å: Chain D: Q.111, C.149 Chain F: G.226, G.227, F.228, G.229, R.342, M.468, G.469, Q.470, A.508, A.509, S.510, V.511, S.512, Q.624, G.690, E.691 Ligands: MOS.11 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain F Hydrogen bonds: D:Q.111, F:G.227, F:F.228, F:M.468, F:Q.470, F:S.510, F:S.512, F:S.512, F:Q.624, F:Q.624 Water bridges: F:R.342, F:T.513, F:T.513

2 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.5: 13 residues within 4Å: Chain C: Q.197, F.228, G.229, E.232, A.340, F.341, R.342, T.507, A.508, A.509, E.691 Ligands: MTE.4, QUE.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.197, C:A.509 MOS.11: 12 residues within 4Å: Chain F: Q.197, G.229, E.232, A.340, F.341, R.342, T.507, A.508, A.509, E.691 Ligands: MTE.10, QUE.12 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.197, F:E.232, F:A.509

2 x QUE: 3,5,7,3',4'-PENTAHYDROXYFLAVONE(Non-covalent)

QUE.6: 15 residues within 4Å: Chain C: L.78, E.232, L.303, S.306, R.310, F.344, S.438, F.439, T.440, V.441, L.444, P.506, A.508, A.509 Ligands: MOS.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.303, C:V.441, C:L.444, C:A.509 Hydrogen bonds: C:E.232, C:R.310, C:R.310, C:T.440, C:A.509 pi-Stacking: C:F.344, C:F.439, C:F.439 QUE.12: 15 residues within 4Å: Chain F: L.78, E.232, L.303, S.306, R.310, F.344, S.438, F.439, T.440, V.441, L.444, P.506, A.508, A.509 Ligands: MOS.11 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:L.303, F:V.441, F:L.444, F:A.509 Hydrogen bonds: F:E.232, F:R.310, F:R.310, F:T.440, F:A.509 Water bridges: F:E.691, F:E.691 pi-Stacking: F:F.344, F:F.439, F:F.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., X-ray Crystal Structure of a Xanthine Oxidase Complex with the Flavonoid Inhibitor Quercetin. J Nat Prod (2014)

Release Date

2011-01-19

Peptides

Xanthine dehydrogenase/oxidase: AD
Xanthine dehydrogenase/oxidase: BE
Xanthine dehydrogenase/oxidase: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
J

B
B

E
K

C
C

F
L

Xanthine dehydrogenase/oxidase

Xanthine dehydrogenase/oxidase

Xanthine dehydrogenase/oxidase

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