SMTL ID : 6ad4.1

Rat Xanthine oxidoreductase, D428A variant, NADH bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x URC: URIC ACID(Non-covalent)

URC.1: 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 9 PLIP interactions: 9 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:L.1011 pi-Stacking: A:F.914, A:F.914 URC.9: 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 9 PLIP interactions: 9 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:L.1011 pi-Stacking: B:F.914, B:F.914

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

BCT.2: 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.10: 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:H.840, B:F.911, B:F.911

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

FES.3: 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.4: 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.7: 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.8: 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.5: 30 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.429 Ligands: NAI.6 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:A.337, A:V.341 Hydrogen bonds: A:K.255, 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:S.346, A:N.350, A:D.359, A:D.359, A:D.359, A:L.403, A:L.403 Water bridges: A:S.346, A:N.350, A:T.353 pi-Stacking: A:F.336 FAD.11: 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, 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 Ligands: NAI.12 28 PLIP interactions: 28 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:E.262, B:I.263, B:A.337, B:S.346, B:N.350, B:D.359, B:D.359, B:L.403, B:L.403, B:K.421 Water bridges: 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.6: 19 residues within 4Å: Chain A: E.262, S.355, P.356, I.357, Y.392, R.393, A.428, D.429, I.430, G.457, A.459, D.460, L.495, P.500, G.501, R.507, S.1225, K.1228 Ligands: FAD.5 16 PLIP interactions: 16 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, A:K.1228 Water bridges: A:E.45, A:E.45, A:A.431, A:G.457, A:R.507 Salt bridges: A:K.270, A:R.393, A:R.393 NAI.12: 20 residues within 4Å: Chain B: E.262, K.270, S.355, P.356, I.357, Y.392, R.393, A.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.11 16 PLIP interactions: 16 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:A.431, B:G.457, B:D.460, B:D.460, B:K.1228 Salt bridges: B:K.270, B:R.393, B:R.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okamoto, K. et al., Rat Xanthine oxidoreductase, D428A variant, NAD bound form. To Be Published

Release Date

2019-07-31

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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