SMTL ID : 3ld4.1

Urate oxidase complexed with 8-nitro xanthine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

4 x 8NX: 8-nitro-3,7-dihydro-1H-purine-2,6-dione(Non-covalent)

8NX.1: 13 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Chain B: Y.9, K.11, I.55, A.57, T.58, D.59 12 PLIP interactions: 9 interactions with chain A, 3 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 Water bridges: A:H.257, B:T.58, B:T.58 pi-Stacking: A:F.160, A:F.160 8NX.4: 13 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 12 PLIP interactions: 9 interactions with chain B, 3 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 Water bridges: B:H.257, A:T.58, A:T.58 pi-Stacking: B:F.160, B:F.160 8NX.7: 13 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Chain D: Y.9, K.11, I.55, A.57, T.58, D.59 9 PLIP interactions: 8 interactions with chain C, 1 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 pi-Stacking: C:F.160, C:F.160 8NX.10: 13 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 9 PLIP interactions: 8 interactions with chain D, 1 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 pi-Stacking: D:F.160, D:F.160

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: E.247, T.248, G.294, R.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.295 EDO.5: 4 residues within 4Å: Chain B: E.247, T.248, G.294, R.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.295 EDO.8: 4 residues within 4Å: Chain C: E.247, T.248, G.294, R.295 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.295 EDO.11: 4 residues within 4Å: Chain D: E.247, T.248, G.294, R.295 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.295

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

NA.3: 5 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:I.95 NA.6: 5 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.92, B:I.95 NA.9: 5 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.89, C:I.95, C:H.96 NA.12: 5 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.93, D:I.95, D:H.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabison, L. et al., Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-06-02

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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