SMTL ID : 1wyg.2 (1 other biounit)

Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: Q.1040, T.1077, A.1078, S.1080, A.1081, S.1082, A.1083 Ligands: ACY.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1080, A:S.1082, A:S.1082, A:A.1083 PO4.2: 4 residues within 4Å: Chain A: P.937, A.938, K.981, D.1276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.938 Water bridges: A:E.939 Salt bridges: A:K.981 PO4.3: 2 residues within 4Å: Chain A: T.611, R.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.611 Salt bridges: A:R.612 PO4.10: 8 residues within 4Å: Chain B: Q.1040, T.1077, A.1078, S.1080, A.1081, S.1082, A.1083 Ligands: ACY.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.1080, B:S.1082, B:S.1082, B:A.1083 PO4.11: 4 residues within 4Å: Chain B: P.937, A.938, K.981, D.1276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.938 Water bridges: B:E.939 Salt bridges: B:K.981 PO4.12: 2 residues within 4Å: Chain B: T.611, R.612 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.611 Salt bridges: B:R.612

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: G.867, T.870, E.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.867, A:T.870, A:S.874, A:S.907, A:N.908 CA.13: 7 residues within 4Å: Chain B: G.867, T.870, E.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.867, B:T.870, B:S.874, B:S.907, B:N.908

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

FES.5: 9 residues within 4Å: Chain A: Q.111, C.112, G.113, C.115, C.147, R.148, C.149, T.150, L.744 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.112, A:C.115, A:C.147, A:C.149 FES.6: 10 residues within 4Å: Chain A: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.43, A:C.48, A:C.51, A:C.73 FES.14: 9 residues within 4Å: Chain B: Q.111, C.112, G.113, C.115, C.147, R.148, C.149, T.150, L.744 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.112, B:C.115, B:C.147, B:C.149 FES.15: 10 residues within 4Å: Chain B: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.43, B:C.48, B:C.51, B:C.73

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

FAD.7: 32 residues within 4Å: Chain A: E.45, G.46, G.47, K.255, L.256, V.257, V.258, G.259, N.260, T.261, E.262, I.263, A.300, L.304, W.335, F.336, A.337, V.341, V.344, A.345, S.346, G.349, N.350, I.352, T.353, S.358, D.359, I.402, L.403, K.421, D.428, D.429 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.337 Hydrogen bonds: A:L.256, A:L.256, A:V.258, A:G.259, A:N.260, A:T.261, A:T.261, A:E.262, A:I.263, A:A.337, A:S.346, A:N.350, A:D.359, A:D.359, A:L.403, A:L.403 Water bridges: A:K.421, A:K.421 pi-Stacking: A:F.336 FAD.16: 32 residues within 4Å: Chain B: E.45, G.46, G.47, K.255, L.256, V.257, V.258, G.259, N.260, T.261, E.262, I.263, A.300, L.304, W.335, F.336, A.337, V.341, V.344, A.345, S.346, G.349, N.350, I.352, T.353, S.358, D.359, I.402, L.403, K.421, D.428, D.429 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:A.337 Hydrogen bonds: B:L.256, B:L.256, B:V.258, B:G.259, B:N.260, B:T.261, B:E.262, B:I.263, B:A.337, B:S.346, B:N.350, B:T.353, B:D.359, B:D.359, B:L.403, B:L.403 Water bridges: B:K.421, B:K.421 pi-Stacking: B:F.336

2 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.8: 11 residues within 4Å: Chain A: E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.914, A:F.1009, A:A.1078, A:A.1079 Hydrogen bonds: A:E.802, A:S.876, A:R.880, A:T.1010 pi-Stacking: A:F.914 SAL.17: 11 residues within 4Å: Chain B: E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.914, B:F.1009, B:A.1078, B:A.1079 Hydrogen bonds: B:E.802, B:S.876, B:R.880, B:T.1010 pi-Stacking: B:F.914

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 5 residues within 4Å: Chain A: A.1078, A.1079, S.1080, E.1261 Ligands: PO4.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1080 ACY.18: 5 residues within 4Å: Chain B: A.1078, A.1079, S.1080, E.1261 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.1080, B:E.1261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishino, T. et al., Mechanism of the Conversion of Xanthine Dehydrogenase to Xanthine Oxidase: IDENTIFICATION OF THE TWO CYSTEINE DISULFIDE BONDS AND CRYSTAL STRUCTURE OF A NON-CONVERTIBLE RAT LIVER XANTHINE DEHYDROGENASE MUTANT. J.Biol.Chem. (2005)

Release Date

2005-05-31

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Xanthine dehydrogenase/oxidase

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