SMTL ID : 7a0l.1

Joint neutron/X-ray room temperature structure of perdeuterated Aspergillus flavus urate oxidase in complex with the 8-azaxanthine inhibitor and catalytic water bound in the peroxo hole

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x AZA: 8-AZAXANTHINE(Non-covalent)

AZA.1: 14 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, H.257, I.289 Chain B: Y.9, I.55, A.57, T.58, D.59 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:T.58, B:T.58, B:D.59, A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255 pi-Stacking: A:F.160 AZA.3: 14 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, H.257, I.289 10 PLIP interactions: 7 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, A:T.58, A:D.59 pi-Stacking: B:F.160 AZA.5: 14 residues within 4Å: Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, H.257, I.289 Chain D: Y.9, I.55, A.57, T.58, D.59 10 PLIP interactions: 7 interactions with chain C, 3 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, D:T.58, D:D.59 pi-Stacking: C:F.160 AZA.7: 14 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, H.257, I.289 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:T.58, C:T.58, C:D.59, D:R.177, D:R.177, D:V.228, D:Q.229, D:Q.229, D:N.255 pi-Stacking: D:F.160

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

NA.2: 6 residues within 4Å: Chain A: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.95, A:H.96, A:E.137 NA.4: 6 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.89, B:I.95, B:H.96 NA.6: 6 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.95, C:H.96, C:E.137 NA.8: 6 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, H.96, E.137 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.95, D:H.96, D:E.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, L. et al., Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. Iucrj (2021)

Release Date

2020-12-09

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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