SMTL ID : 3nvz.1

Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3-Aldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 8 residues within 4Å: Chain D: Q.111, C.112, G.113, C.115, C.147, R.148, C.149 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.33, L.34, V.35, V.36, G.37, N.38, T.39, E.40, I.41, A.78, L.82, F.114, A.115, V.119, V.122, A.123, S.124, G.127, N.128, I.130, T.131, S.136, D.137, I.180, L.181 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.115, B:V.119, B:V.119 Hydrogen bonds: B:L.34, B:L.34, B:V.36, B:G.37, B:N.38, B:T.39, B:E.40, B:I.41, B:S.124, B:D.137, B:D.137, B:D.137, B:L.181, B:L.181 Water bridges: B:K.33, B:T.39, B:E.40, B:E.44, B:S.124, B:R.203, B:K.210 pi-Stacking: B:F.114 FAD.9: 25 residues within 4Å: Chain D: E.44, G.45 Chain E: K.33, L.34, V.35, V.36, G.37, N.38, T.39, E.40, I.41, A.78, F.114, A.115, V.119, A.123, S.124, G.127, N.128, I.130, T.131, S.136, D.137, I.180, L.181 26 PLIP interactions: 26 interactions with chain E Hydrophobic interactions: E:A.115, E:V.119, E:V.119 Hydrogen bonds: E:L.34, E:L.34, E:V.36, E:G.37, E:N.38, E:T.39, E:T.39, E:E.40, E:I.41, E:A.115, E:S.124, E:N.128, E:D.137, E:D.137, E:L.181, E:L.181 Water bridges: E:E.44, E:S.124, E:T.131, E:R.203, E:K.210, E:K.210 pi-Stacking: E:F.114

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: 18 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, E.691 Ligands: MOS.5 13 PLIP interactions: 12 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: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 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.227, F:F.228, F:M.468, F:Q.470, F:S.512, F:S.512, F:S.512, F:Q.624, F:Q.624, D:Q.111 Water bridges: F:R.342, F:G.690

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

MOS.5: 12 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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.197, C:A.509 MOS.11: 13 residues within 4Å: Chain F: Q.197, F.228, G.229, E.232, A.340, F.341, R.342, T.507, A.508, A.509, E.691 Ligands: MTE.10, I3A.12 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.197, F:E.232, F:A.509

2 x I3A: 1H-INDOLE-3-CARBALDEHYDE(Non-covalent)

I3A.6: 10 residues within 4Å: Chain C: E.232, L.303, S.306, R.310, F.344, S.438, F.439, T.440, V.441, L.444 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.303, C:F.344, C:F.439, C:V.441, C:L.444 Hydrogen bonds: C:E.232, C:R.310, C:T.440 pi-Stacking: C:F.344, C:F.439 I3A.12: 12 residues within 4Å: Chain F: E.232, L.303, S.306, R.310, F.344, S.438, F.439, T.440, V.441, L.444, A.509 Ligands: MOS.11 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.303, F:F.344, F:F.439, F:V.441, F:L.444 Hydrogen bonds: F:E.232, F:R.310, F:T.440 pi-Stacking: F:F.344, F:F.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., Substrate orientation and specificity in xanthine oxidase: crystal structures of the enzyme in complex with indole-3-acetaldehyde and guanine. Biochemistry (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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