SMTL ID : 2e3t.1

Crystal structure of rat xanthine oxidoreductase mutant (W335A and F336L)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

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

BCT.1: 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 BCT.14: 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:T.909, B:F.911, B:F.911, B:F.914, B:G.915

11 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: T.611, R.612 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.611 Salt bridges: A:R.612 PO4.3: 7 residues within 4Å: Chain A: Q.1040, L.1042, T.1077, A.1078, S.1080, A.1081, S.1082 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.1040, A:A.1078, A:S.1082 Water bridges: A:T.1077, A:S.1080, A:S.1080, A:A.1083, A:A.1083, A:G.1260, A:G.1260 PO4.4: 5 residues within 4Å: Chain A: K.421, R.425, K.432, K.1228 Ligands: FAD.12 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.424 Salt bridges: A:K.421, A:R.425, A:K.432, A:K.1228 PO4.5: 5 residues within 4Å: Chain A: R.426, G.502, M.503, H.1212, E.1302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.503 Salt bridges: A:R.426 PO4.6: 5 residues within 4Å: Chain A: P.937, A.938, E.939, Y.977, D.1276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.938, A:D.1276 PO4.7: 2 residues within 4Å: Chain A: F.1293, Q.1294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1294 PO4.15: 7 residues within 4Å: Chain B: Q.1040, L.1042, T.1077, A.1078, S.1080, A.1081, S.1082 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.1040, B:S.1082 Water bridges: B:A.1083, B:A.1083 PO4.16: 6 residues within 4Å: Chain B: K.421, S.424, R.425, K.432, K.1228 Ligands: FAD.24 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.424 Water bridges: B:K.421, B:K.421, B:R.425 Salt bridges: B:K.421, B:R.425, B:K.432, B:K.1228 PO4.17: 4 residues within 4Å: Chain B: R.426, G.502, M.503, H.1212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.503 Water bridges: B:V.504 Salt bridges: B:R.426 PO4.18: 6 residues within 4Å: Chain B: L.936, P.937, A.938, E.939, K.981, D.1276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.938, B:Y.977, B:Y.977 PO4.19: 3 residues within 4Å: Chain B: Q.1291, F.1293, Q.1294 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.1291, B:Q.1294 Water bridges: B:R.1282, B:L.1292, B:Q.1294, B:Q.1294

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 7 residues within 4Å: Chain A: G.867, T.870, E.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.867, A:E.871, A:S.874, A:S.907, A:N.908 CA.9: 6 residues within 4Å: Chain A: E.740, 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:E.740, A:H.741, A:Y.743, A:G.837, H2O.23 CA.20: 7 residues within 4Å: Chain B: G.867, T.870, E.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.867, B:E.871, B:S.874, B:S.907, B:N.908 CA.21: 5 residues within 4Å: Chain B: E.740, H.741, Y.743, T.836, G.837 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.740, B:H.741, B:T.836, B:G.837, H2O.50

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

FES.10: 8 residues within 4Å: Chain A: Q.111, C.112, G.113, C.115, C.147, R.148, C.149, L.744 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.112, A:C.115, A:C.147, A:C.149 FES.11: 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.22: 8 residues within 4Å: Chain B: Q.111, C.112, G.113, C.115, C.147, R.148, C.149, L.744 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.112, B:C.115, B:C.147, B:C.149 FES.23: 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 FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 29 residues within 4Å: Chain A: E.45, G.46, G.47, K.255, L.256, V.257, V.258, G.259, N.260, T.261, E.262, I.263, A.300, L.304, L.336, A.337, V.344, A.345, S.346, G.349, N.350, I.352, T.353, S.358, D.359, I.402, L.403, K.421 Ligands: PO4.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:A.337 Hydrogen bonds: A:L.256, A:L.256, A:V.258, A:G.259, A:N.260, A:T.261, A:T.261, A:E.262, A:I.263, A:A.337, A:V.344, A:S.346, A:N.350, A:D.359, A:D.359, A:L.360, A:L.403, A:L.403, A:K.421 Water bridges: A:T.261, A:E.262, A:S.346, A:R.425 FAD.24: 30 residues within 4Å: Chain B: E.45, G.46, G.47, K.255, L.256, V.257, V.258, G.259, N.260, T.261, E.262, I.263, A.300, L.304, L.336, A.337, V.341, V.344, A.345, S.346, G.349, N.350, I.352, T.353, S.358, D.359, I.402, L.403, K.421 Ligands: PO4.16 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.337 Hydrogen bonds: B:L.256, B:L.256, B:V.258, B:G.259, B:N.260, B:T.261, B:T.261, B:E.262, B:I.263, B:A.337, B:V.344, B:S.346, B:N.350, B:T.353, B:D.359, B:D.359, B:D.359, B:L.360, B:L.403, B:L.403, B:K.421 Water bridges: B:K.255, B:T.261, B:E.262, B:E.266, B:E.266, B:S.346

2 x URC: URIC ACID(Non-covalent)

URC.13: 9 residues within 4Å: Chain A: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.880, A:T.1010, A:A.1079, A:E.1261 Water bridges: A:E.802, A:E.802, A:T.1010, A:L.1011 pi-Stacking: A:F.914, A:F.914 URC.25: 9 residues within 4Å: Chain B: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.880, B:T.1010, B:A.1079, B:E.1261 Water bridges: B:T.1010, B:L.1011 pi-Stacking: B:F.914, B:F.914

Links

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Citation

Asai, R. et al., Two mutations convert mammalian xanthine oxidoreductase to highly superoxide-productive xanthine oxidase. J.Biochem.(Tokyo) (2007)

Release Date

2007-09-25

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase