SMTL ID : 4n9m.1

Joint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x 8HX: 8-hydroxy-3,9-dihydro-1H-purine-2,6-dione(Non-covalent)

8HX.1: 15 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Chain B: Y.9, K.11, I.55, A.57, T.58, D.59 Ligands: CL.2 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255, B:T.58, B:T.58, B:D.59 pi-Stacking: A:F.160, A:F.160 Water bridges: B:K.11, B:D.59 8HX.4: 15 residues within 4Å: Chain A: Y.9, K.11, I.55, A.57, T.58, D.59 Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Ligands: CL.5 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.177, B:R.177, B:V.228, B:Q.229, B:Q.229, B:N.255, A:T.58, A:T.58, A:D.59 pi-Stacking: B:F.160, B:F.160 Water bridges: A:K.11, A:D.59 8HX.7: 15 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Chain D: Y.9, K.11, I.55, A.57, T.58, D.59 Ligands: CL.8 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:T.58, D:T.58, D:D.59, C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255 Water bridges: D:K.11, D:D.59 pi-Stacking: C:F.160, C:F.160 8HX.10: 15 residues within 4Å: Chain C: Y.9, K.11, I.55, A.57, T.58, D.59 Chain D: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Ligands: CL.11 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:R.177, D:R.177, D:V.228, D:Q.229, D:Q.229, D:N.255, C:T.58, C:T.58, C:D.59 pi-Stacking: D:F.160, D:F.160 Water bridges: C:K.11, C:D.59

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: N.255, H.257, G.287, I.289 Chain B: T.58 Ligands: 8HX.1 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: T.58 Chain B: N.255, H.257, G.287, I.289 Ligands: 8HX.4 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain C: N.255, H.257, G.287, I.289 Chain D: T.58 Ligands: 8HX.7 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain C: T.58 Chain D: N.255, H.257, G.287, I.289 Ligands: 8HX.10 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.95, A:H.96, A:E.137 NA.6: 6 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.89, B:I.95, B:H.96 NA.9: 6 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.89, C:I.95, C:H.96 NA.12: 6 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.95, D:H.96, D:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oksanen, E. et al., The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. Plos One (2014)

Release Date

2014-02-05

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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