SMTL ID : 3bjp.1

Urate oxidase cyanide uric acid ternary complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: I.88, Y.91, N.92, I.94, E.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.92, A:I.94 NA.5: 5 residues within 4Å: Chain B: I.88, Y.91, N.92, I.94, E.136 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.91, B:I.94 NA.9: 5 residues within 4Å: Chain C: I.88, Y.91, N.92, I.94, E.136 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.94, C:I.94 NA.13: 5 residues within 4Å: Chain D: I.88, Y.91, N.92, I.94, E.136 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.94, D:E.136

4 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 6 residues within 4Å: Chain A: N.254, H.256, G.286, I.288 Chain B: T.57 Ligands: URC.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.254, B:T.57 CYN.6: 6 residues within 4Å: Chain A: T.57 Chain B: N.254, H.256, G.286, I.288 Ligands: URC.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.254, A:T.57 CYN.10: 6 residues within 4Å: Chain C: N.254, H.256, G.286, I.288 Chain D: T.57 Ligands: URC.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.254 CYN.14: 6 residues within 4Å: Chain C: T.57 Chain D: N.254, H.256, G.286, I.288 Ligands: URC.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.254

4 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.3: 3 residues within 4Å: Chain A: S.1 Chain B: R.294, S.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.295 ACE.7: 3 residues within 4Å: Chain A: R.294, S.295 Chain B: S.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.295 ACE.11: 3 residues within 4Å: Chain C: S.1 Chain D: R.294, S.295 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.295 ACE.15: 3 residues within 4Å: Chain C: R.294, S.295 Chain D: S.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.295

4 x URC: URIC ACID(Non-covalent)

URC.4: 14 residues within 4Å: Chain A: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Chain B: Y.8, I.54, A.56, T.57, D.58 Ligands: CYN.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.176, A:R.176, A:V.227, A:Q.228, A:Q.228, A:N.254, B:T.57, B:D.58 pi-Stacking: A:F.159, A:F.159 Water bridges: B:K.10 URC.8: 14 residues within 4Å: Chain A: Y.8, I.54, A.56, T.57, D.58 Chain B: F.159, L.170, R.176, S.226, V.227, Q.228, N.254, I.288 Ligands: CYN.6 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.176, B:R.176, B:V.227, B:Q.228, B:Q.228, B:N.254, A:T.57, A:D.58 pi-Stacking: B:F.159, B:F.159 Water bridges: A:K.10 URC.12: 14 residues within 4Å: Chain C: 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: CYN.10 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:R.176, C:R.176, C:V.227, C:Q.228, C:Q.228, C:N.254, D:T.57, D:D.58 pi-Stacking: C:F.159, C:F.159 Water bridges: D:K.10, D:T.57 URC.16: 14 residues within 4Å: Chain C: 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: CYN.14 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.176, D:R.176, D:V.227, D:Q.228, D:Q.228, D:N.254, C:T.57, C:D.58 pi-Stacking: D:F.159, D:F.159 Water bridges: C:K.10, C:T.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabison, L. et al., Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: Mechanistic implications. Bmc Struct.Biol. (2008)

Release Date

2008-08-12

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Uricase

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