SMTL ID : 3bdj.1

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.867, A:S.870, A:S.874, A:S.907, A:N.908 CA.12: 7 residues within 4Å: Chain B: A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.867, B:S.870, B:S.874, B:S.907, B:N.908

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

FES.2: 8 residues within 4Å: Chain A: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.113, A:C.116, A:C.148, A:C.150 FES.3: 11 residues within 4Å: Chain A: L.41, 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.13: 8 residues within 4Å: Chain B: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.116, B:C.148, B:C.150 FES.14: 11 residues within 4Å: Chain B: L.41, 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 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: 20 residues within 4Å: Chain A: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 Ligands: MOW.5, 141.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.112, A:G.797, A:F.798, A:M.1038, A:Q.1040, A:S.1082, A:S.1082, A:S.1082, A:Q.1194, A:Q.1194 Water bridges: A:R.912, A:T.1083, A:T.1083, A:G.1260 MTE.15: 20 residues within 4Å: Chain B: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 Ligands: MOW.16, 141.18 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.112, B:G.797, B:F.798, B:M.1038, B:Q.1040, B:S.1082, B:S.1082, B:S.1082, B:Q.1194, B:Q.1194 Water bridges: B:R.912, B:R.912, B:G.1260

2 x MOW: Oxo(sulfanyl)molybdenum(IV) ION(Non-covalent)

MOW.5: 10 residues within 4Å: Chain A: Q.767, G.799, E.802, A.910, F.911, R.912, A.1078, E.1261 Ligands: MTE.4, 141.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.767 MOW.16: 13 residues within 4Å: Chain B: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, G.913, T.1077, A.1078, E.1261 Ligands: MTE.15, 141.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.767

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

FAD.6: 32 residues within 4Å: Chain A: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, A.301, W.336, F.337, A.338, V.342, A.346, S.347, G.349, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338 Hydrogen bonds: A:L.257, A:L.257, A:V.259, A:G.260, A:N.261, A:T.262, A:E.263, A:E.263, A:E.263, A:I.264, A:A.338, A:S.347, A:N.351, A:D.360, A:D.360, A:L.404, A:L.404 Water bridges: A:K.256, A:E.267, A:S.347, A:K.422, A:K.422, A:D.429 pi-Stacking: A:F.337 FAD.17: 32 residues within 4Å: Chain B: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, A.301, W.336, F.337, A.338, V.342, A.346, S.347, G.349, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338 Hydrogen bonds: B:L.257, B:V.259, B:G.260, B:N.261, B:T.262, B:T.262, B:E.263, B:E.263, B:I.264, B:A.338, B:S.347, B:N.351, B:T.354, B:D.360, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:S.347, B:K.422, B:A.432 pi-Stacking: B:F.337

2 x 141: Oxypurinol(Non-covalent)

141.7: 11 residues within 4Å: Chain A: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 Ligands: MTE.4, MOW.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.1078 Hydrogen bonds: A:R.880, A:T.1010, A:A.1079, A:E.1261 Water bridges: A:E.802, A:V.1011 pi-Stacking: A:F.914 141.18: 11 residues within 4Å: Chain B: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 Ligands: MTE.15, MOW.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.1078 Hydrogen bonds: B:R.880, B:T.1010, B:A.1079, B:E.1261 Water bridges: B:E.802, B:V.1011 pi-Stacking: B:F.914

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: C.662, G.664, H.665, I.666, R.804, I.835, N.869, S.906, S.907 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.666, A:R.804, A:N.869, A:N.869, A:S.907 Water bridges: A:S.870 GOL.9: 6 residues within 4Å: Chain A: D.594, F.604, P.675, R.824, C.825, M.826 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.594, A:M.826, A:M.826 Water bridges: A:R.31, A:R.32, A:L.605 GOL.10: 10 residues within 4Å: Chain A: E.759, M.760, N.785, R.786, I.787, L.788, N.1069 Chain B: L.1030, Y.1062, S.1064 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.759, A:M.760, A:N.785, A:I.787, B:S.1064 GOL.19: 6 residues within 4Å: Chain B: D.594, F.604, P.675, R.824, C.825, M.826 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.594, B:M.826, B:M.826 Water bridges: B:R.31, B:L.605 GOL.20: 10 residues within 4Å: Chain B: C.662, G.664, H.665, I.666, R.804, L.807, I.835, N.869, S.906, S.907 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.665, B:I.666, B:R.804, B:N.869, B:S.907 Water bridges: B:R.804, B:I.835 GOL.21: 6 residues within 4Å: Chain B: Q.561, E.562, G.574, S.1184, S.1185, P.1188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.574, B:S.1185 Water bridges: B:V.563 GOL.22: 6 residues within 4Å: Chain B: L.580, A.581, H.1043, V.1047, Y.1062, I.1063 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:E.756, B:I.1061, B:Y.1062 Hydrogen bonds: B:I.1063

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.11: 9 residues within 4Å: Chain A: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.839, A:F.911, A:G.915, A:Q.918 CO3.23: 9 residues within 4Å: Chain B: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.840, B:F.911, B:F.911, B:G.915

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol. Nucleosides Nucleotides Nucleic Acids (2008)

Release Date

2008-11-25

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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