SMTL ID : 3pli.1

Urate oxidase under 1.8 MPa / 18 bars pressure of equimolar mixture xenon : nitrous oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

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

AZA.1: 12 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 12 PLIP interactions: 8 interactions with chain A, 4 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 Water bridges: B:T.58, B:T.58 AZA.6: 12 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 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.58, A:D.59, B:R.177, B:R.177, B:V.228, B:Q.229, B:Q.229, B:N.255 Water bridges: A:T.58, A:T.58 pi-Stacking: B:F.160, B:F.160 AZA.11: 12 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 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.16: 12 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 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.7: 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.12: 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:Y.92, C:H.96 NA.17: 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:N.93, D:H.96

8 x XE: XENON(Non-covalent)

XE.3: 3 residues within 4Å: Chain A: T.231, L.253 Ligands: N2O.5 No protein-ligand interaction detected (PLIP) XE.4: 4 residues within 4Å: Chain A: V.16, K.18, Y.31, M.33 No protein-ligand interaction detected (PLIP) XE.8: 3 residues within 4Å: Chain B: T.231, L.253 Ligands: N2O.10 No protein-ligand interaction detected (PLIP) XE.9: 4 residues within 4Å: Chain B: V.16, K.18, Y.31, M.33 No protein-ligand interaction detected (PLIP) XE.13: 3 residues within 4Å: Chain C: T.231, L.253 Ligands: N2O.15 No protein-ligand interaction detected (PLIP) XE.14: 4 residues within 4Å: Chain C: V.16, K.18, Y.31, M.33 No protein-ligand interaction detected (PLIP) XE.18: 3 residues within 4Å: Chain D: T.231, L.253 Ligands: N2O.20 No protein-ligand interaction detected (PLIP) XE.19: 4 residues within 4Å: Chain D: V.16, K.18, Y.31, M.33 No protein-ligand interaction detected (PLIP)

4 x N2O: NITROUS OXIDE(Non-covalent)

N2O.5: 9 residues within 4Å: Chain A: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 Ligands: XE.3 No protein-ligand interaction detected (PLIP) N2O.10: 9 residues within 4Å: Chain B: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 Ligands: XE.8 No protein-ligand interaction detected (PLIP) N2O.15: 9 residues within 4Å: Chain C: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 Ligands: XE.13 No protein-ligand interaction detected (PLIP) N2O.20: 9 residues within 4Å: Chain D: L.179, T.181, F.220, V.228, T.231, M.232, M.235, L.253 Ligands: XE.18 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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