SMTL ID : 4ysw.1

Structure of rat xanthine oxidoreductase, C-terminal deletion protein variant, NADH bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 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

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 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

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

FAD.4: 31 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, 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.428, D.429 Ligands: NAI.5 27 PLIP interactions: 27 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:E.262, 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 Water bridges: A:K.255, A:E.266, A:S.346, A:K.421, A:K.421, A:K.421 pi-Stacking: A:F.336 FAD.12: 30 residues within 4Å: Chain B: E.45, G.46, 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.428, D.429 Ligands: NAI.13 30 PLIP interactions: 30 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:E.262, B:E.262, B:I.263, B:A.337, B:S.346, B:N.350, B:N.350, B:T.353, B:D.359, B:D.359, B:D.359, B:L.403, B:L.403 Water bridges: B:K.255, B:K.255, B:K.255, B:K.255, B:E.266, B:E.266, B:S.346, B:T.353 pi-Stacking: B:F.336

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

NAI.5: 20 residues within 4Å: Chain A: E.262, K.270, S.355, P.356, I.357, Y.392, R.393, D.428, D.429, I.430, G.457, M.458, A.459, D.460, L.495, P.500, G.501, R.507, S.1225 Ligands: FAD.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.430 Hydrogen bonds: A:E.262, A:Y.392, A:Y.392, A:R.393, A:R.393, A:R.507 Water bridges: A:E.45, A:E.45, A:K.270, A:K.270, A:K.270, A:K.270, A:K.432, A:K.432, A:G.457, A:R.507, A:K.1228 Salt bridges: A:K.270, A:R.393, A:R.393 NAI.13: 19 residues within 4Å: Chain B: E.262, K.270, S.355, P.356, I.357, Y.392, R.393, D.428, D.429, I.430, G.457, M.458, A.459, D.460, P.500, G.501, R.507, S.1225 Ligands: FAD.12 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.430 Hydrogen bonds: B:E.262, B:Y.392, B:R.393, B:R.393, B:R.507 Water bridges: B:E.45, B:E.45, B:E.45, B:E.45, B:E.262, B:E.262, B:K.270, B:K.270, B:G.457, B:D.460, B:R.507, B:K.1228 Salt bridges: B:K.270, B:R.393, B:R.393

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 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.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:R.839, B:F.911, B:F.914, B:G.915, B:Q.918

2 x URC: URIC ACID(Non-covalent)

URC.7: 9 residues within 4Å: Chain A: E.802, R.880, F.914, S.1008, F.1009, T.1010, A.1078, A.1079, E.1261 13 PLIP interactions: 13 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:E.802, A:R.912, A:T.1010, A:L.1011 pi-Stacking: A:F.914, A:F.914 URC.15: 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 GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: E.652, C.662, G.664, H.665, I.666, R.804, I.835, N.869, P.906, S.907 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.666, A:R.804, A:N.869, A:S.907 Water bridges: A:I.835, A:S.907 GOL.16: 9 residues within 4Å: Chain B: C.662, G.664, H.665, I.666, R.804, I.835, N.869, P.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

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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