SMTL ID : 4cw3.1

Crystal structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-metyl uric acid (X-ray dose, 665 kGy)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-tetramer

Ligands

4 x XDS: (5S)-5-(dioxidanyl)-9-methyl-7H-purine-2,6,8-trione(Non-covalent)

XDS.1: 17 residues within 4Å: Chain A: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, H.256, G.286, I.288 Chain C: Y.8, I.54, A.56, T.57, D.58 Ligands: OXY.3, MUA.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.176, A:R.176, A:V.227, A:Q.228, A:Q.228, A:N.254, C:T.57, C:T.57, C:D.58 XDS.5: 17 residues within 4Å: Chain B: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, H.256, G.286, I.288 Chain D: Y.8, I.54, A.56, T.57, D.58 Ligands: OXY.7, MUA.8 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:T.57, D:D.58, B:R.176, B:R.176, B:V.227, B:Q.228, B:Q.228, B:N.254 XDS.9: 17 residues within 4Å: Chain A: Y.8, I.54, A.56, T.57, D.58 Chain C: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, H.256, G.286, I.288 Ligands: OXY.11, MUA.12 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:T.57, A:T.57, A:D.58, C:R.176, C:R.176, C:V.227, C:Q.228, C:Q.228, C:N.254 XDS.13: 17 residues within 4Å: Chain B: Y.8, I.54, A.56, T.57, D.58 Chain D: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, H.256, G.286, I.288 Ligands: OXY.15, MUA.16 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.176, D:R.176, D:V.227, D:Q.228, D:Q.228, D:N.254, B:T.57, B:D.58

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

MPD.2: 4 residues within 4Å: Chain A: Q.158, W.160, W.174, N.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.158 Water bridges: A:N.223, A:N.223 MPD.6: 4 residues within 4Å: Chain B: Q.158, W.160, W.174, N.223 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.158 Water bridges: B:N.223, B:N.223 MPD.10: 4 residues within 4Å: Chain C: Q.158, W.160, W.174, N.223 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.158 Water bridges: C:N.223, C:N.223 MPD.14: 4 residues within 4Å: Chain D: Q.158, W.160, W.174, N.223 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.158 Water bridges: D:N.223, D:N.223

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 7 residues within 4Å: Chain A: N.254, H.256, G.286, I.288 Chain C: T.57 Ligands: XDS.1, MUA.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.254, A:H.256, A:G.286, C:T.57, C:T.57 OXY.7: 7 residues within 4Å: Chain B: N.254, H.256, G.286, I.288 Chain D: T.57 Ligands: XDS.5, MUA.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.254, B:H.256, B:G.286 OXY.11: 7 residues within 4Å: Chain A: T.57 Chain C: N.254, H.256, G.286, I.288 Ligands: XDS.9, MUA.12 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.254, C:H.256, C:G.286, A:T.57, A:T.57 OXY.15: 7 residues within 4Å: Chain B: T.57 Chain D: N.254, H.256, G.286, I.288 Ligands: XDS.13, MUA.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.254, D:H.256, D:G.286, B:T.57

4 x MUA: 9-METHYL URIC ACID(Non-covalent)

MUA.4: 15 residues within 4Å: Chain A: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Chain C: Y.8, I.54, A.56, T.57, D.58 Ligands: XDS.1, OXY.3 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.176, A:R.176, A:V.227, A:Q.228, A:Q.228, A:N.254, C:T.57, C:D.58 pi-Stacking: A:F.159, A:F.159 MUA.8: 15 residues within 4Å: Chain B: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Chain D: Y.8, I.54, A.56, T.57, D.58 Ligands: XDS.5, OXY.7 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain B Hydrogen bonds: D:T.57, D:D.58, B:R.176, B:R.176, B:V.227, B:Q.228, B:Q.228, B:N.254 pi-Stacking: B:F.159, B:F.159 MUA.12: 15 residues within 4Å: Chain A: Y.8, I.54, A.56, T.57, D.58 Chain C: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Ligands: XDS.9, OXY.11 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:T.57, A:D.58, C:R.176, C:R.176, C:V.227, C:Q.228, C:Q.228, C:N.254 pi-Stacking: C:F.159, C:F.159 MUA.16: 15 residues within 4Å: Chain B: Y.8, I.54, A.56, T.57, D.58 Chain D: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Ligands: XDS.13, OXY.15 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.176, D:R.176, D:V.227, D:Q.228, D:Q.228, D:N.254, B:T.57, B:D.58 pi-Stacking: D:F.159, D:F.159

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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