SMTL ID : 3ax7.1

Bovine Xanthine Oxidase, protease cleaved form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 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: 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.11: 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.12: 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 FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 27 residues within 4Å: Chain A: E.45, G.46, 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:A.338, A:V.342, 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:S.347, A:N.351, A:D.360, A:D.360, A:L.404, A:L.404, A:K.422 Water bridges: A:E.267, A:S.347 pi-Stacking: A:F.337 FAD.13: 26 residues within 4Å: Chain B: E.45, G.46, 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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.338, B:V.342, B:V.342 Hydrogen bonds: 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:I.264, B:S.347, B:N.351, B:D.360, B:D.360, B:L.404, B:L.404 pi-Stacking: B:F.337

2 x XAX: {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum(Non-covalent)

XAX.4: 23 residues within 4Å: Chain A: Q.112, C.150, Q.767, G.796, G.797, F.798, G.799, E.802, F.911, R.912, G.913, M.1038, G.1039, Q.1040, T.1077, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.112, A:Q.767, A:G.797, A:F.798, A:E.802, A:M.1038, A:Q.1040, A:A.1079, A:S.1080, A:S.1082, A:S.1082, A:Q.1194, A:Q.1194 Water bridges: A:R.912, A:R.912, A:T.1083, A:G.1260 XAX.14: 23 residues within 4Å: Chain B: Q.112, C.150, Q.767, G.796, G.797, F.798, G.799, E.802, F.911, R.912, G.913, M.1038, G.1039, Q.1040, T.1077, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.112, B:Q.767, B:G.797, B:F.798, B:E.802, B:E.802, B:M.1038, B:Q.1040, B:A.1079, B:S.1080, B:S.1082, B:Q.1194, B:Q.1194 Water bridges: B:R.912, B:G.1260

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

SAL.5: 10 residues within 4Å: Chain A: E.802, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1079 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1014, A:A.1079 Hydrogen bonds: A:S.876, A:T.1010, A:T.1010, A:V.1011 Salt bridges: A:R.880 pi-Stacking: A:F.914, A:F.1009 SAL.15: 11 residues within 4Å: Chain B: E.802, S.876, R.880, F.914, S.1008, F.1009, T.1010, V.1011, L.1014, A.1078, A.1079 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.1014, B:A.1078, B:A.1079 Hydrogen bonds: B:S.876, B:T.1010, B:T.1010, B:T.1010, B:V.1011 Salt bridges: B:R.880 pi-Stacking: B:F.914, B:F.1009

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.839, A:F.911, A:G.915, A:Q.918 BCT.16: 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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:D.594, A:M.826, A:M.826 Water bridges: A:L.605 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.664, A:I.666, A:R.804, A:N.869, A:S.907 Water bridges: A:I.835, A:S.907 GOL.9: 4 residues within 4Å: Chain A: E.45, I.266, F.270, N.830 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.45 Water bridges: A:E.45, A:S.1225, A:S.1225 GOL.17: 6 residues within 4Å: Chain B: R.32, D.594, F.604, R.824, C.825, M.826 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.32, B:M.826 Water bridges: B:R.31, B:L.605, B:L.605 GOL.18: 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:R.804, B:I.835

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.19: 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

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

2012-02-22

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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