SMTL ID : 3l9g.1

Urate oxidase complexed with uric acid and chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x URC: URIC ACID(Non-covalent)

URC.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, I.55, A.57, T.58, D.59 Ligands: CL.3 10 PLIP interactions: 8 interactions with chain A, 2 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:D.59 pi-Stacking: A:F.160, A:F.160 URC.5: 13 residues within 4Å: Chain A: Y.9, I.55, A.57, T.58, D.59 Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Ligands: CL.7 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 URC.9: 13 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Chain D: Y.9, I.55, A.57, T.58, D.59 Ligands: CL.11 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:T.58, D:D.59, C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255 pi-Stacking: C:F.160, C:F.160 URC.13: 13 residues within 4Å: Chain C: Y.9, I.55, A.57, T.58, D.59 Chain D: F.160, L.171, R.177, S.227, V.228, Q.229, N.255 Ligands: CL.15 10 PLIP interactions: 8 interactions with chain D, 2 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:D.59 pi-Stacking: D:F.160, D:F.160

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 4 residues within 4Å: Chain A: K.5, A.6, G.41, E.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.44 Hydrogen bonds: A:G.41 Water bridges: A:G.41, A:G.41 MRD.6: 4 residues within 4Å: Chain B: K.5, A.6, G.41, E.44 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.44 Hydrogen bonds: B:G.41 Water bridges: B:G.41, B:G.41 MRD.10: 4 residues within 4Å: Chain C: K.5, A.6, G.41, E.44 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.44 Hydrogen bonds: C:G.41 Water bridges: C:G.41, C:G.41 MRD.14: 4 residues within 4Å: Chain D: K.5, A.6, G.41, E.44 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:E.44 Hydrogen bonds: D:G.41 Water bridges: D:G.41, D:G.41

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

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

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

NA.4: 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:I.95, A:E.137 NA.8: 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:I.89, B:I.95 NA.12: 5 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.89, C:I.95 NA.16: 5 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, E.137 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.93, D:I.95

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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