SMTL ID : 4n9s.1

High resolution X-RAY STRUCTURE OF URATE OXIDASE IN COMPLEX WITH 8-HYDROXYXANTHINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 7 residues within 4Å: Chain A: N.255, H.257, G.287, I.289 Chain B: K.11, T.58 Ligands: 8HX.3 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain A: K.11, T.58 Chain B: N.255, H.257, G.287, I.289 Ligands: 8HX.7 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain C: N.255, H.257, G.287, I.289 Chain D: K.11, T.58 Ligands: 8HX.11 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain C: K.11, T.58 Chain D: N.255, H.257, G.287, I.289 Ligands: 8HX.15 Ligand excluded by PLIP

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

NA.2: 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:N.93, A:I.95, A:H.96 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:Y.92, B:I.95, B:H.96 NA.10: 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.95, C:I.95, C:H.96 NA.14: 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

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

8HX.3: 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.1 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.58, B:D.59, A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255 pi-Stacking: A:F.160, A:F.160 8HX.7: 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 10 PLIP interactions: 8 interactions with chain B, 2 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:D.59 pi-Stacking: B:F.160, B:F.160 8HX.11: 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.9 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255, D:T.58, D:D.59 pi-Stacking: C:F.160, C:F.160 8HX.15: 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.13 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:T.58, C:D.59, D:R.177, D:R.177, D:V.228, D:Q.229, D:Q.229, D:N.255 pi-Stacking: D:F.160, D:F.160

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.283, D.284, P.285 Chain B: R.15 Chain C: P.281, Q.282, S.283, D.284 Ligands: GOL.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.283, C:S.283, C:D.284, C:D.284 Water bridges: C:Q.282, C:Q.282, C:Q.282, C:Q.282 GOL.8: 9 residues within 4Å: Chain A: R.15 Chain B: S.283, D.284, P.285 Chain D: P.281, Q.282, S.283, D.284 Ligands: GOL.16 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.283, D:S.283, D:D.284, D:D.284 Water bridges: D:Q.282, D:Q.282, D:Q.282, D:Q.282 GOL.12: 9 residues within 4Å: Chain A: P.281, Q.282, S.283, D.284 Chain C: S.283, D.284, P.285 Chain D: R.15 Ligands: GOL.4 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:D.284, A:S.283, A:S.283, A:D.284, A:D.284 Water bridges: A:Q.282, A:Q.282, A:Q.282, A:Q.282 GOL.16: 9 residues within 4Å: Chain B: P.281, Q.282, S.283, D.284 Chain C: R.15 Chain D: S.283, D.284, P.285 Ligands: GOL.8 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.283, B:S.283, B:D.284, B:D.284, D:D.284 Water bridges: B:Q.282, B:Q.282, B:Q.282, B:Q.282

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

Related Entries With Identical Sequence