SMTL ID : 3una.1

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NAD Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.18: 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.19: 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.3: 21 residues within 4Å: Chain A: Q.112, C.113, 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, T.1083, Q.1194, G.1260, E.1261 Ligands: MOS.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.112, A:C.113, 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.20: 21 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, L.1042, A.1078, A.1079, S.1080, V.1081, S.1082, T.1083, Q.1194, G.1260, E.1261 Ligands: MOS.21 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.112, B:C.113, B:G.797, B:F.798, B:M.1038, B:Q.1040, B:S.1082, B:S.1082, B:S.1082, B:T.1083, B:T.1083, B:Q.1194, B:Q.1194 Water bridges: B:R.912, B:R.912, B:V.1259, 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, SAL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.767, A:A.1079 MOS.21: 12 residues within 4Å: Chain B: Q.767, F.798, G.799, E.802, F.911, R.912, T.1077, A.1078, A.1079, E.1261 Ligands: MTE.20, SAL.25 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.5: 34 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, W.336, F.337, A.338, V.342, A.346, S.347, G.349, G.350, N.351, I.353, T.354, I.358, 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, A:V.342 Hydrogen bonds: A:L.257, A:L.257, A:V.259, A:G.260, A:N.261, A:T.262, A:T.262, A:E.263, A:E.263, A:I.264, A:A.338, A:S.347, A:N.351, A:T.354, A:D.360, A:D.360, A:D.360, A:L.404, A:L.404 Water bridges: A:K.256, A:E.267, A:S.347 pi-Stacking: A:F.337 FAD.22: 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, B:V.342 Hydrogen bonds: B:L.257, B:L.257, B:V.259, B:G.260, B:N.261, B:T.262, B:E.263, B:E.263, B:E.263, B:I.264, B:A.338, B:S.347, B:N.351, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:S.347, B:D.429, B:A.432 pi-Stacking: B:F.337

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 12 residues within 4Å: Chain A: P.357, I.358, Y.393, R.394, G.458, A.460, D.461, L.496, A.500, P.501, G.502, R.508 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.393, A:P.501, A:R.508 Water bridges: A:D.461, A:D.461 Salt bridges: A:R.394 NAD.23: 11 residues within 4Å: Chain B: P.357, I.358, Y.393, R.394, G.458, A.460, D.461, A.500, P.501, G.502, R.508 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.501, B:R.508 Water bridges: B:D.461, B:D.461 Salt bridges: B:R.394

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

CO3.7: 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:H.840, A:T.909, A:Q.918, A:Q.918 CO3.24: 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:T.909, B:F.911, B:F.911, B:G.915

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

SAL.8: 12 residues within 4Å: Chain A: E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 Ligands: MOS.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.873, A:F.914, A:F.914, A:V.1011, A:L.1014 Hydrogen bonds: A:T.1010, A:T.1010, A:A.1079 Salt bridges: A:R.880 pi-Stacking: A:F.1009 SAL.25: 12 residues within 4Å: Chain B: E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 Ligands: MOS.21 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.873, B:F.914, B:F.914, B:V.1011, B:L.1014 Hydrogen bonds: B:T.1010, B:T.1010, B:A.1079 Salt bridges: B:R.880 pi-Stacking: B:F.1009

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 10 residues within 4Å: Chain A: C.662, G.664, H.665, I.666, R.804, L.807, I.835, N.869, S.906, S.907 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.666, A:R.804, A:N.869, A:N.869, A:S.907 GOL.10: 4 residues within 4Å: Chain A: Q.1088, Y.1091, I.1253, Y.1254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.1088, A:Y.1254 Water bridges: A:E.1092 GOL.11: 7 residues within 4Å: Chain A: L.580, I.1058, S.1059, I.1061, Y.1062 Chain B: E.757, R.786 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.757, B:R.786, A:I.1061 GOL.12: 7 residues within 4Å: Chain A: R.606, L.607, V.608, T.609, E.679, A.682, H.683 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.606, A:T.609, A:T.609, A:E.679 Water bridges: A:R.606, A:L.607 GOL.13: 4 residues within 4Å: Chain A: Q.561, G.574, S.1184, S.1185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.574, A:S.1185 Water bridges: A:V.563 GOL.14: 7 residues within 4Å: Chain A: R.32, D.594, F.604, P.675, R.824, C.825, M.826 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.32, A:D.594, A:M.826, A:M.826 Water bridges: A:R.31, A:L.605 GOL.15: 11 residues within 4Å: Chain A: E.761, L.788, R.790, E.1065, S.1067, N.1069 Chain B: E.761, R.790, E.1065, S.1067, N.1069 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.790, B:S.1067, B:S.1067, B:N.1069, A:E.1065, A:S.1067, A:S.1067, A:N.1069 GOL.16: 9 residues within 4Å: Chain A: E.759, M.760, N.785, R.786, I.787, L.788 Chain B: L.1030, Y.1062, S.1064 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.759, B:S.1064 Water bridges: A:K.754, A:E.759, A:E.759, A:M.760, A:I.787 GOL.26: 9 residues within 4Å: Chain B: C.662, G.664, H.665, I.666, R.804, I.835, N.869, S.906, S.907 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.666, B:R.804, B:N.869, B:N.869, B:S.907 Water bridges: B:I.835, B:S.907 GOL.27: 7 residues within 4Å: Chain B: R.32, D.594, F.604, P.675, R.824, C.825, M.826 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.32, B:D.594, B:M.826, B:M.826 Water bridges: B:R.31 GOL.28: 5 residues within 4Å: Chain B: Q.1088, Y.1091, A.1252, I.1253, Y.1254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.1088, B:Q.1088, B:A.1252, B:Y.1254 GOL.29: 5 residues within 4Å: Chain B: Q.561, 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.30: 10 residues within 4Å: Chain A: L.1030, Y.1062, S.1064 Chain B: E.759, M.760, N.785, R.786, I.787, L.788, N.1069 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.1064, B:E.759, B:M.760, B:M.760, B:N.785, B:I.787

2 x CA: CALCIUM ION(Non-covalent)

CA.17: 8 residues within 4Å: Chain A: H.840, 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.31: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishikita, H. et al., Protein conformational gating of enzymatic activity in xanthine oxidoreductase. J.Am.Chem.Soc. (2012)

Release Date

2012-05-09

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

Related Entries With Identical Sequence