SMTL ID : 3uni.1

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NADH Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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.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.3: 21 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, L.1042, A.1078, A.1079, S.1080, V.1081, S.1082, T.1083, Q.1194, G.1260, E.1261 Ligands: MOS.4 16 PLIP interactions: 16 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:A.1078, A:T.1083, A:G.1260 MTE.16: 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.17 15 PLIP interactions: 15 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:Q.1194, B:Q.1194 Water bridges: B:R.912, B:T.1083, 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, G.913, A.1078, A.1079, E.1261 Ligands: MTE.3, SAL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.767, A:E.802, A:A.1079 MOS.17: 12 residues within 4Å: Chain B: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, A.1078, A.1079, E.1261 Ligands: MTE.16, SAL.26 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: 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, L.287, A.301, W.336, 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 Ligands: NAI.6 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338, A:V.342 Hydrogen bonds: A:K.256, 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:A.338, A:S.347, A:N.351, A:N.351, A:T.354, A:D.360, A:D.360, A:D.360, A:L.404, A:L.404 Water bridges: A:S.347 pi-Stacking: A:F.337 FAD.18: 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, L.305, W.336, 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 Ligands: NAI.19 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338, B:V.342 Hydrogen bonds: B:K.256, B:L.257, 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:E.263, B:I.264, B:A.338, B:S.347, B:N.351, B:T.354, B:D.360, B:D.360, B:L.404, B:L.404 Water bridges: B:S.347, B:D.429, B:D.430 pi-Stacking: B:F.337

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.6: 19 residues within 4Å: Chain A: E.263, K.271, S.356, P.357, I.358, Y.393, R.394, D.429, D.430, I.431, G.458, A.460, D.461, A.500, P.501, G.502, R.508, S.1225 Ligands: FAD.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.431 Hydrogen bonds: A:E.263, A:Y.393, A:R.394, A:R.394, A:R.508 Water bridges: A:E.45, A:E.45, A:S.356, A:A.432, A:G.458, A:D.461, A:R.508, A:K.1228 Salt bridges: A:K.271, A:R.394, A:R.394 NAI.19: 20 residues within 4Å: Chain B: E.263, K.271, S.356, P.357, I.358, Y.393, R.394, D.429, D.430, I.431, G.458, A.460, D.461, L.496, A.500, P.501, G.502, R.508, S.1225 Ligands: FAD.18 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.431 Hydrogen bonds: B:E.263, B:R.394, B:R.508 Water bridges: B:E.45, B:E.45, B:R.394, B:K.433, B:K.433, B:G.458, B:K.1228 Salt bridges: B:K.271, B:R.394, B:R.394

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: W.336, K.422, Q.423, R.427, F.549, D.1170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.423, A:D.1170 Water bridges: A:D.1170 GOL.8: 6 residues within 4Å: Chain A: L.580, A.581, R.793, H.1043, Y.1062, I.1063 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.793, A:I.1063 Water bridges: A:I.1061, A:I.1063 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.666, A:R.804, A:N.869, A:N.869, A:S.907 Water bridges: A:V.654, A:R.804, A:I.835 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:M.826 Water bridges: A:R.31, A:L.605, A:R.824 GOL.20: 6 residues within 4Å: Chain B: L.580, A.581, R.793, V.1047, Y.1062, I.1063 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.793, B:I.1063 Water bridges: B:I.1061, B:I.1063 GOL.21: 6 residues within 4Å: Chain B: D.594, F.604, P.675, R.824, C.825, M.826 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.594, B:M.826, B:M.826 Water bridges: B:R.31 GOL.22: 9 residues within 4Å: Chain B: C.662, G.664, H.665, I.666, R.804, I.835, N.869, S.906, S.907 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.665, B:I.666, B:R.804, B:N.869, B:S.907 Water bridges: B:I.835, B:S.870, B:S.907 GOL.23: 8 residues within 4Å: Chain B: R.427, F.549, K.994, E.1163, D.1165, D.1170, H.1171, K.1172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.1163, B:E.1163, B:H.1171 GOL.24: 7 residues within 4Å: Chain B: Q.561, V.563, P.564, G.574, S.1184, S.1185, P.1188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.574, B:S.1184 Water bridges: B:V.563

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 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 CO3.25: 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:R.839, B:F.911, B:G.915, B:Q.918

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

SAL.12: 10 residues within 4Å: Chain A: E.802, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 Ligands: MOS.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: 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.26: 11 residues within 4Å: Chain B: E.802, L.873, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 Ligands: MOS.17 9 PLIP interactions: 9 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 Salt bridges: B:R.880 pi-Stacking: B:F.1009

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.27: 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:R.871, 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

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