SMTL ID : 8j79.1

Bovine Xanthine Oxidoreductase Crystallized with oxypurinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 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.2: 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.12: 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.13: 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 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.3: 19 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: MOS.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.112, A:G.797, A:F.798, A:M.1038, A:Q.1040, A:S.1080, A:S.1082, A:S.1082, A:Q.1194, A:Q.1194 Water bridges: A:R.912, A:G.1260 MTE.14: 19 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: MOS.15 12 PLIP interactions: 12 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:Q.1194, B:Q.1194 Water bridges: B:R.912, B:Q.1040, B:G.1260

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

MOS.4: 13 residues within 4Å: Chain A: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, T.1077, A.1078, A.1079, E.1261 Ligands: MTE.3, 141.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.767, A:E.802, A:A.1079 MOS.15: 13 residues within 4Å: Chain B: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, T.1077, A.1078, A.1079, E.1261 Ligands: MTE.14, 141.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.767, B:A.1079

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

FAD.5: 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, 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 Ligands: GOL.11 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338, A:V.342 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:S.347, A:K.422, A:K.422, A:K.422, A:K.422 pi-Stacking: A:F.337 FAD.16: 33 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 Ligands: GOL.21 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338, B:V.342 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:K.256, B:K.256, B:K.256, B:E.267, B:E.267, B:S.347, B:T.354 pi-Stacking: B:F.337

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

CO3.6: 9 residues within 4Å: Chain A: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.840, A:H.840, A:T.909, A:Q.918, A:Q.918 CO3.17: 9 residues within 4Å: Chain B: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.839, B:F.911, B:F.914, B:G.915, B:Q.918

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.8: 5 residues within 4Å: Chain A: H.741, Y.743, D.832, T.836, G.837 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.741, A:Y.743, A:T.836, A:G.837, H2O.16 CA.18: 8 residues within 4Å: Chain B: H.840, 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 CA.19: 6 residues within 4Å: Chain B: D.740, H.741, Y.743, D.832, T.836, G.837 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.741, B:Y.743, B:T.836, B:G.837, H2O.42

2 x 141: Oxypurinol(Non-covalent)

141.9: 11 residues within 4Å: Chain A: E.802, R.880, A.910, F.914, S.1008, F.1009, T.1010, L.1014, A.1078, A.1079 Ligands: MOS.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1009 Hydrogen bonds: A:E.802, A:R.880, A:T.1010, A:A.1079 pi-Stacking: A:F.914, A:F.914 141.20: 9 residues within 4Å: Chain B: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079 Ligands: MOS.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.802, B:R.880, B:T.1010, B:A.1079 pi-Stacking: B:F.914, B:F.914, B:F.1009

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: E.45, I.266, F.270, K.271, N.830, R.1222, G.1223, S.1225 Ligands: GOL.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.271, A:K.271, A:N.830, A:S.1225 Water bridges: A:E.45, A:R.1222, A:G.1223 GOL.11: 5 residues within 4Å: Chain A: E.45, I.431, S.1225 Ligands: FAD.5, GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.45, A:S.1225 Water bridges: A:E.45, A:D.429, A:I.431 GOL.21: 5 residues within 4Å: Chain B: E.45, I.431, S.1225 Ligands: FAD.16, GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.1225 Water bridges: B:D.429, B:D.430 GOL.22: 8 residues within 4Å: Chain B: E.45, I.266, F.270, N.830, R.1222, G.1223, S.1225 Ligands: GOL.21 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.1225 Water bridges: B:E.45, B:E.45, B:R.1222, B:G.1223, B:S.1225, B:S.1225 GOL.23: 6 residues within 4Å: Chain B: F.68, A.304, S.306, S.307, S.344 Ligands: GOL.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.306 Water bridges: B:S.306, B:S.307, B:S.307, B:S.307 GOL.24: 7 residues within 4Å: Chain B: F.68, V.259, A.302, A.304, S.344, V.345 Ligands: GOL.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.259, B:A.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., Bovine Xanthine Oxidoreductase Crystallized with oxypurinol. To Be Published

Release Date

2023-05-24

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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