SMTL ID : 4d13.1

Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 2.2 kGy)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

4 x IUP: 5-(HYDRO)PEROXOISOURATE(Non-covalent)

IUP.1: 15 residues within 4Å: Chain A: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, H.257, G.287, I.289 Chain C: Y.9, I.55, A.57, T.58, D.59 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.177, A:R.177, A:V.228, A:Q.229, A:Q.229, A:N.255, C:T.58, C:T.58, C:D.59 Water bridges: A:H.257 IUP.3: 15 residues within 4Å: Chain B: F.160, L.171, R.177, S.227, V.228, Q.229, N.255, H.257, G.287, I.289 Chain D: Y.9, I.55, A.57, T.58, D.59 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.177, B:R.177, B:V.228, B:Q.229, B:Q.229, B:N.255, D:T.58, D:D.59 Water bridges: B:H.257 IUP.5: 15 residues within 4Å: Chain A: 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, H.257, G.287, I.289 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:T.58, A:T.58, A:D.59, C:R.177, C:R.177, C:V.228, C:Q.229, C:Q.229, C:N.255 Water bridges: C:H.257 IUP.7: 15 residues within 4Å: Chain B: 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, G.287, I.289 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.177, D:R.177, D:V.228, D:Q.229, D:Q.229, D:N.255, B:T.58, B:D.59 Water bridges: D:H.257

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 4 residues within 4Å: Chain A: Q.159, W.161, W.175, N.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.159 Water bridges: A:N.224, A:N.224 MPD.4: 4 residues within 4Å: Chain B: Q.159, W.161, W.175, N.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.159 Water bridges: B:N.224, B:N.224 MPD.6: 4 residues within 4Å: Chain C: Q.159, W.161, W.175, N.224 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.159 Water bridges: C:N.224, C:N.224 MPD.8: 4 residues within 4Å: Chain D: Q.159, W.161, W.175, N.224 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.159 Water bridges: D:N.224, D:N.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bui, S. et al., Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Angew. Chem. Int. Ed. Engl. (2014)

Release Date

2014-10-29

Peptides

URICASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

URICASE

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