SMTL ID : 6adj.1

Rat Xanthine oxidoreductase, D428E variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 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: 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.5: 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.6: 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:T.870, A:S.874, A:S.907, A:N.908 CA.7: 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

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

FAD.4: 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, 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, E.428, D.429 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.337, A:V.341 Hydrogen bonds: 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:L.403, A:L.403, A:K.421 Water bridges: A:T.261, A:E.262, A:S.346 pi-Stacking: A:F.336 FAD.8: 28 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.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 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:A.337, B:V.341, 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:S.346, B:N.350, B:T.353, B:D.359, B:D.359, B:D.359, B:L.403, B:L.403, B:K.421 Water bridges: B:K.255, B:E.262, B:E.262, B:E.266, B:A.337, B:S.346 pi-Stacking: B:F.336

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

2019-08-07

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase