SMTL ID : 3lbg.1

Urate oxidase complexed with 8-thio xanthine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

8 x 8TX: 8-thioxo-3,7,8,9-tetrahydro-1H-purine-2,6-dione(Non-covalent)

8TX.1: 13 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, I.55, A.57, T.58, D.59 11 PLIP interactions: 8 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 pi-Stacking: A:F.160, A:F.160 Water bridges: B:T.58, B:T.58 8TX.2: 5 residues within 4Å: Chain A: D.12, C.36, N.101, Q.132 Ligands: TRS.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.101, A:N.101, A:Q.132 8TX.9: 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, I.289 11 PLIP interactions: 8 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 pi-Stacking: B:F.160, B:F.160 Water bridges: A:T.58, A:T.58 8TX.10: 5 residues within 4Å: Chain B: D.12, C.36, N.101, Q.132 Ligands: TRS.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.101, B:N.101, B:Q.132 8TX.17: 13 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, I.55, A.57, T.58, D.59 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:T.58, 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 8TX.18: 5 residues within 4Å: Chain C: D.12, C.36, N.101, Q.132 Ligands: TRS.19 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.101, C:N.101, C:Q.132 8TX.25: 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, I.289 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:T.58, 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 8TX.26: 5 residues within 4Å: Chain D: D.12, C.36, N.101, Q.132 Ligands: TRS.27 3 PLIP interactions: 3 interactions with chain D Water bridges: D:N.101, D:N.101, D:Q.132

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: D.12, N.13, T.34, C.36, N.101, V.103 Ligands: 8TX.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.13, A:N.101 Water bridges: A:D.12, A:N.13, A:C.36, A:N.101, A:N.101 TRS.11: 7 residues within 4Å: Chain B: D.12, N.13, T.34, C.36, N.101, V.103 Ligands: 8TX.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.13, B:N.101 Water bridges: B:D.12, B:N.13, B:C.36, B:N.101, B:N.101 TRS.19: 7 residues within 4Å: Chain C: D.12, N.13, T.34, C.36, N.101, V.103 Ligands: 8TX.18 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.13, C:N.101 Water bridges: C:D.12, C:N.13, C:C.36, C:N.101, C:N.101 TRS.27: 7 residues within 4Å: Chain D: D.12, N.13, T.34, C.36, N.101, V.103 Ligands: 8TX.26 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.13, D:N.101 Water bridges: D:D.12, D:N.13, D:C.36, D:N.101, D:N.101

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

EDO.4: 1 residues within 4Å: Chain A: C.104 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: Q.159, W.161, W.175 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: R.15, E.32, H.105 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: T.25, G.26, P.118 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain B: C.104 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: Q.159, W.161, W.175 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: R.15, E.32, H.105 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: T.25, G.26, P.118 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain C: C.104 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: Q.159, W.161, W.175 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain C: R.15, E.32, H.105 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain C: T.25, G.26, P.118 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain D: C.104 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain D: Q.159, W.161, W.175 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain D: R.15, E.32, H.105 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain D: T.25, G.26, P.118 Ligand excluded by PLIP

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

NA.8: 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.16: 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.24: 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:Y.92, C:I.95 NA.32: 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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