SMTL ID : 4fsk.1

Urate oxidase-azide complex in anaerobic conditions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

12 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: AZI.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.58, B:T.58, A:Q.229, A:Q.229 Water bridges: B:D.59, B:D.59, A:N.255, A:N.255 AZI.2: 8 residues within 4Å: Chain A: V.228, N.255, H.257, G.287, I.289 Chain B: K.11, T.58 Ligands: AZI.1 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.11, B:T.58, B:T.58, A:N.255 Water bridges: B:D.59, A:R.177, A:R.177 AZI.3: 4 residues within 4Å: Chain A: D.176, R.177, E.260, F.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.260 Water bridges: A:T.174, A:I.178, A:I.178 AZI.5: 6 residues within 4Å: Chain A: I.55, A.57, T.58 Chain B: F.160, Q.229 Ligands: AZI.6 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.58, A:T.58, B:Q.229 Water bridges: A:D.59, A:D.59, B:Q.229, B:N.255, B:N.255 AZI.6: 8 residues within 4Å: Chain A: K.11, T.58 Chain B: V.228, N.255, H.257, G.287, I.289 Ligands: AZI.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.11, A:T.58, B:N.255 Water bridges: A:D.59, B:R.177, B:R.177 AZI.7: 4 residues within 4Å: Chain B: D.176, R.177, E.260, F.279 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.260 Water bridges: B:T.174, B:I.178, B:I.178, B:A.276 AZI.9: 6 residues within 4Å: Chain C: F.160, Q.229 Chain D: I.55, A.57, T.58 Ligands: AZI.10 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.229, D:T.58, D:T.58 Water bridges: C:Q.229, C:N.255, C:N.255, D:D.59, D:D.59 AZI.10: 8 residues within 4Å: Chain C: V.228, N.255, H.257, G.287, I.289 Chain D: K.11, T.58 Ligands: AZI.9 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.255, C:H.257, D:K.11 Water bridges: C:R.177, C:R.177, C:Q.229, D:D.59 AZI.11: 4 residues within 4Å: Chain C: D.176, R.177, E.260, F.279 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.260 Water bridges: C:T.174, C:D.176, C:I.178, C:I.178 AZI.13: 6 residues within 4Å: Chain C: I.55, A.57, T.58 Chain D: F.160, Q.229 Ligands: AZI.14 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.229, D:Q.229, C:T.58 Water bridges: D:N.255, D:N.255, C:D.59, C:D.59 AZI.14: 8 residues within 4Å: Chain C: K.11, T.58 Chain D: V.228, N.255, H.257, G.287, I.289 Ligands: AZI.13 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.255, D:H.257, C:K.11 Water bridges: D:R.177, D:R.177, D:Q.229, C:D.59 AZI.15: 4 residues within 4Å: Chain D: D.176, R.177, E.260, F.279 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.260 Water bridges: D:T.174, D:I.178, D:I.178

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:I.95, D:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2013-07-03

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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