SMTL ID : 4ytz.1

Rat xanthine oxidoreductase, C-terminal deletion protein variant, crystal grown without dithiothreitol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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.8: 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.9: 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: 26 residues within 4Å: Chain A: E.45, G.46, K.255, L.256, V.257, V.258, G.259, N.260, T.261, E.262, I.263, A.300, 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.337, A:V.341, 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:S.346, A:N.350, A:N.350, A:D.359, A:D.359, A:D.359, A:L.403, A:L.403 pi-Stacking: A:F.336 FAD.10: 26 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, F.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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.337 Hydrogen bonds: B:L.256, B:V.258, B:G.259, B:N.260, B:T.261, B:E.262, B:I.263, B:S.346, B:D.359, B:D.359, B:L.403, B:L.403 pi-Stacking: B:F.336, B:F.336

2 x URC: URIC ACID(Non-covalent)

URC.4: 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.802, A:R.880, A:R.880, A:T.1010, A:A.1079, A:E.1261 pi-Stacking: A:F.914, A:F.914 URC.11: 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 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.802, B:R.880, B:R.880, B:T.1010, B:A.1079, B:E.1261 pi-Stacking: B:F.914, B:F.914

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

BCT.5: 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:R.839, A:F.911, A:F.914, A:G.915, A:Q.918 BCT.12: 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

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.7: 6 residues within 4Å: Chain A: E.740, H.741, Y.743, D.832, T.836, G.837 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.740, A:H.741, A:Y.743, A:T.836, A:G.837 CA.13: 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:T.870, B:S.874, B:S.907, B:N.908 CA.14: 5 residues within 4Å: Chain B: E.740, H.741, Y.743, T.836, G.837 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.740, B:H.741, B:Y.743, B:T.836, B:G.837

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishino, T. et al., The C-terminal peptide plays a role in the formation of an intermediate form during the transition between xanthine dehydrogenase and xanthine oxidase. Febs J. (2015)

Release Date

2015-04-22

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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