SMTL ID : 3p9o.1

Aerobic ternary complex of urate oxidase with azide and chloride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

16 x AZI: AZIDE ION(Non-covalent)

AZI.1: 6 residues within 4Å: Chain A: F.160, Q.229 Chain B: I.55, A.57, T.58 Ligands: CL.5 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.58, A:Q.229, A:Q.229 Water bridges: B:D.59, A:N.255, A:N.255 AZI.2: 5 residues within 4Å: Chain A: A.6, A.7, R.8 Chain B: K.290, C.291 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.6, A:R.8, A:R.8 Water bridges: A:A.7 AZI.3: 6 residues within 4Å: Chain A: D.142, I.143, Q.188, W.189, K.190, N.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.143, A:Q.188, A:W.189, A:W.189 Water bridges: A:N.191, A:F.192 AZI.4: 1 residues within 4Å: Chain A: Q.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.159 AZI.7: 6 residues within 4Å: Chain A: I.55, A.57, T.58 Chain B: F.160, Q.229 Ligands: CL.11 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.58, B:Q.229, B:Q.229 Water bridges: A:T.58, A:D.59, B:N.255, B:N.255 AZI.8: 5 residues within 4Å: Chain A: K.290, C.291 Chain B: A.6, A.7, R.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.6, B:A.7, B:R.8, B:R.8 Water bridges: B:A.7 AZI.9: 6 residues within 4Å: Chain B: D.142, I.143, Q.188, W.189, K.190, N.191 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.142, B:I.143, B:Q.188, B:W.189 Water bridges: B:N.191, B:F.192 AZI.10: 1 residues within 4Å: Chain B: Q.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.159 Water bridges: B:N.224 AZI.13: 6 residues within 4Å: Chain C: F.160, Q.229 Chain D: I.55, A.57, T.58 Ligands: CL.17 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.58, C:Q.229 Water bridges: D:T.58, D:D.59, C:N.255 AZI.14: 5 residues within 4Å: Chain C: A.6, A.7, R.8 Chain D: K.290, C.291 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Water bridges: D:T.292, C:E.40 Hydrogen bonds: C:A.6, C:A.7, C:R.8, C:R.8 AZI.15: 6 residues within 4Å: Chain C: D.142, I.143, Q.188, W.189, K.190, N.191 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.142, C:I.143, C:Q.188, C:W.189 Water bridges: C:I.141, C:N.191, C:F.192 AZI.16: 1 residues within 4Å: Chain C: Q.159 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.159 Water bridges: C:N.224 AZI.19: 6 residues within 4Å: Chain C: I.55, A.57, T.58 Chain D: F.160, Q.229 Ligands: CL.23 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.58, C:T.58, D:Q.229 Water bridges: C:D.59, D:N.255 AZI.20: 5 residues within 4Å: Chain C: K.290, C.291 Chain D: A.6, A.7, R.8 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Water bridges: C:T.292, D:E.40 Hydrogen bonds: D:R.8, D:R.8 AZI.21: 6 residues within 4Å: Chain D: D.142, I.143, Q.188, W.189, K.190, N.191 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.142, D:D.142, D:I.143, D:Q.188, D:W.189 Water bridges: D:N.191, D:F.192 AZI.22: 1 residues within 4Å: Chain D: Q.159 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.159

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

CL.5: 5 residues within 4Å: Chain A: N.255, H.257, G.287 Chain B: T.58 Ligands: AZI.1 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: T.58 Chain B: N.255, H.257, G.287 Ligands: AZI.7 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: N.255, H.257, G.287 Chain D: T.58 Ligands: AZI.13 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain C: T.58 Chain D: N.255, H.257, G.287 Ligands: AZI.19 Ligand excluded by PLIP

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

NA.6: 5 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.93, A:I.95, A:H.96 NA.12: 5 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, E.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.89, B:I.95, B:H.96 NA.18: 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.24: 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:I.95, D:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabison, L. et al., Azide and Cyanide Show Different Inhibition Modes to Urate Oxidase. To be Published

Release Date

2011-08-31

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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