SMTL ID : 3an1.1

Crystal structure of rat D428A mutant, urate bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 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.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.9: 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.10: 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

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.740, H.741, Y.743, T.836, G.837 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.740, A:Y.743, A:T.836, A:G.837, H2O.6 CA.4: 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.11: 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.16: 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:Y.743, B:G.837, H2O.52

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

FAD.5: 30 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, W.335, F.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, D.429 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.337, A:V.341 Hydrogen bonds: A:L.256, A:L.256, A:V.258, A:G.259, A:N.260, A:T.261, A:E.262, A:I.263, A:A.337, A:S.346, A:N.350, A:T.353, A:D.359, A:D.359, A:L.403, A:L.403, A:K.421 Water bridges: A:K.255, A:E.266, A:S.346 pi-Stacking: A:F.336 FAD.12: 29 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, W.335, F.336, A.337, V.341, A.345, S.346, G.349, N.350, I.352, T.353, S.358, D.359, I.402, L.403, K.421, D.429 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.337, B:V.341 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:S.346, B:N.350, B:D.359, B:D.359, B:D.359, B:L.403, B:L.403, B:K.421 Water bridges: B:S.346, B:T.353 pi-Stacking: B:F.336

2 x URC: URIC ACID(Non-covalent)

URC.6: 10 residues within 4Å: Chain A: E.802, R.880, A.910, 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:E.802, A:R.880, A:R.880, A:T.1010, A:A.1079, A:E.1261 Water bridges: A:E.802, A:L.1011 pi-Stacking: A:F.914, A:F.914 URC.13: 10 residues within 4Å: Chain B: E.802, R.880, A.910, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.802, B:R.880, B:R.880, B:T.1010, B:A.1079, B:E.1261 Water bridges: B:Q.767, B:L.1011 pi-Stacking: B:F.914, B:F.914

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

BCT.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.840, A:F.911, A:F.911, A:F.914, A:G.915 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.909, B:F.911, B:F.911

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: Q.561, G.574, S.1184, S.1185, P.1188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.574, A:S.1185 Water bridges: A:E.562, A:V.563 GOL.15: 6 residues within 4Å: Chain B: Q.561, V.563, G.574, S.1184, S.1185, P.1188 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.561, B:Q.561 Water bridges: B:V.563, B:S.1185, B:D.1246, B:D.1246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate. J.Am.Chem.Soc. (2010)

Release Date

2010-12-01

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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