SMTL ID : 5frc.1

Structure of urate oxidase prepared by the 'soak-and-freeze' method under 42 bar of oxygen pressure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 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, I.289 Chain D: Y.9, I.55, A.57, T.58, D.59 Ligands: OXY.3 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255, D:T.58, D:D.59 pi-Stacking: A:F.160, A:F.160 AZA.4: 14 residues within 4Å: Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Chain C: Y.9, I.55, A.57, T.58, D.59 Ligands: OXY.6 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.177, B:R.177, B:V.228, B:Q.229, B:Q.229, B:N.255, C:T.58, C:D.59 pi-Stacking: B:F.160, B:F.160 AZA.7: 14 residues within 4Å: Chain B: Y.9, I.55, A.57, T.58, D.59 Chain C: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, I.289 Ligands: OXY.9 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255, B:T.58, B:D.59 pi-Stacking: C:F.160, C:F.160 AZA.10: 14 residues within 4Å: Chain A: 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, I.289 Ligands: OXY.12 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain D Hydrogen bonds: A:T.58, A: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, D:F.160

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

NA.2: 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:N.93, A:I.95 NA.5: 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:N.93, B:I.95 NA.8: 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.11: 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.89, D:I.95

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 6 residues within 4Å: Chain A: N.255, H.257, G.287, I.289 Chain D: T.58 Ligands: AZA.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.255, D:T.58 OXY.6: 6 residues within 4Å: Chain B: N.255, H.257, G.287, I.289 Chain C: T.58 Ligands: AZA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255 OXY.9: 6 residues within 4Å: Chain B: T.58 Chain C: N.255, H.257, G.287, I.289 Ligands: AZA.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.255 OXY.12: 6 residues within 4Å: Chain A: T.58 Chain D: N.255, H.257, G.287, I.289 Ligands: AZA.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.58, D:N.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lafumat, B. et al., Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. (2016)

Release Date

2016-10-26

Peptides

URICASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

URICASE

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