SMTL ID : 1v97.1

Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 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.13: 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: 9 residues within 4Å: Chain A: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, T.151, 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: 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: 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.15: 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: 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.5 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:T.1083, A:Q.1194, A:Q.1194 Water bridges: A:R.912, A:T.1083, A:G.1260 MTE.16: 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.17 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:S.1082, B:Q.1194, B:Q.1194 Water bridges: B:R.912, B:G.1260

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

MOS.5: 11 residues within 4Å: Chain A: Q.767, G.799, E.802, A.910, F.911, R.912, A.1078, A.1079, E.1261 Ligands: MTE.4, FYX.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.767, A:A.1079 MOS.17: 11 residues within 4Å: Chain B: Q.767, G.799, E.802, A.910, F.911, R.912, A.1078, A.1079, E.1261 Ligands: MTE.16, FYX.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.767, B:E.802, B:A.1079

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

FAD.6: 31 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, L.305, F.337, A.338, V.342, A.346, S.347, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 25 PLIP interactions: 25 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:I.264, A:V.345, A:S.347, A:D.360, A:D.360, A:D.360, A:L.404, A:L.404, A:K.422 Water bridges: A:T.262, A:A.338, A:A.338, A:S.347, A:A.432 pi-Stacking: A:F.337 FAD.18: 31 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, L.305, F.337, A.338, V.342, A.346, S.347, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 23 PLIP interactions: 23 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:I.264, B:A.338, B:S.347, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:E.263, B:E.263, B:S.347, B:D.429, B:A.432 pi-Stacking: B:F.337

2 x FYX: 4-(5-PYRIDIN-4-YL-1H-1,2,4-TRIAZOL-3-YL)PYRIDINE-2-CARBONITRILE(Non-covalent)

FYX.7: 15 residues within 4Å: Chain A: L.648, N.768, K.771, E.802, L.873, S.876, R.880, F.914, F.1009, L.1014, P.1076, A.1078, A.1079, E.1261 Ligands: MOS.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.873, A:F.914, A:L.1014, A:A.1078, A:A.1079 Hydrogen bonds: A:N.768, A:A.1079 Water bridges: A:K.771, A:T.1010, A:T.1010, A:T.1010, A:T.1010 pi-Stacking: A:F.914, A:F.1009 FYX.19: 15 residues within 4Å: Chain B: L.648, N.768, K.771, E.802, L.873, S.876, R.880, F.914, F.1009, L.1014, P.1076, A.1078, A.1079, E.1261 Ligands: MOS.17 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.873, B:F.914, B:L.1014, B:A.1078, B:A.1079 Hydrogen bonds: B:N.768, B:A.1079 Water bridges: B:K.771, B:S.876, B:T.1010, B:T.1010, B:T.1010 pi-Stacking: B:F.914, B:F.1009

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

ACY.8: 9 residues within 4Å: Chain A: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.877, A:F.911 Hydrogen bonds: A:H.840, A:F.911, A:G.915, A:Q.918 Salt bridges: A:R.839, A:H.840 ACY.20: 9 residues within 4Å: Chain B: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.877, B:F.911 Hydrogen bonds: B:H.840, B:T.909, B:G.915, B:Q.918 Salt bridges: B:R.839, B:H.840

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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:H.665, A:I.666, A:R.804, A:N.869, A:S.907 Water bridges: A:S.870 GOL.10: 6 residues within 4Å: Chain A: D.594, F.604, P.675, R.824, C.825, M.826 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.824, A:M.826 Water bridges: A:R.31, A:R.606 GOL.11: 5 residues within 4Å: Chain A: Q.561, G.574, S.1184, S.1185, P.1188 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.561, A:Q.561, A:V.563, A:S.1184 GOL.12: 5 residues within 4Å: Chain A: Q.1088, Y.1091, E.1092, I.1253, Y.1254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.1088, A:Y.1254 GOL.21: 9 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:H.665, B:I.666, B:R.804, B:N.869, B:S.907 Water bridges: B:S.870 GOL.22: 5 residues within 4Å: Chain B: D.594, F.604, R.824, C.825, M.826 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.824, B:M.826 Water bridges: B:R.31, B:R.606, B:M.826 GOL.23: 5 residues within 4Å: Chain B: Q.561, G.574, S.1184, S.1185, P.1188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.561 Water bridges: B:V.563, B:S.1184, B:S.1185 GOL.24: 5 residues within 4Å: Chain B: Q.1088, Y.1091, E.1092, I.1253, Y.1254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.1092, B:Y.1254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-06-22

Peptides

Xanthine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase

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