SMTL ID : 3pku.1

Urate oxidase under 1 MPa / 10 bars pressure of nitrous oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

AZA.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 AZA.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 AZA.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 AZA.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 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.137 NA.6: 6 residues within 4Å: Chain B: I.89, Y.92, N.93, I.95, H.96, E.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.96 NA.10: 6 residues within 4Å: Chain C: I.89, Y.92, N.93, I.95, H.96, E.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.95, C:H.96 NA.14: 6 residues within 4Å: Chain D: I.89, Y.92, N.93, I.95, H.96, E.137 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.96, D:E.137

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

4 x N2O: NITROUS OXIDE(Non-covalent)

N2O.4: 8 residues within 4Å: Chain A: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.228 N2O.8: 8 residues within 4Å: Chain B: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.228 N2O.12: 8 residues within 4Å: Chain C: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 No protein-ligand interaction detected (PLIP) N2O.16: 8 residues within 4Å: Chain D: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marassio, G. et al., Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study. Faseb J. (2011)

Release Date

2011-04-06

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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