SMTL ID : 5yj2.1

Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-tetramer

Ligands

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

AZA.1: 14 residues within 4Å: Chain A: F.177, L.188, R.194, S.241, I.242, Q.243, N.269, Q.297 Chain B: Y.4, V.63, A.65, T.66, D.67 Ligands: OXY.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.194, A:R.194, A:I.242, A:Q.243, A:Q.243, A:N.269, A:Q.297, B:T.66, B:T.66, B:D.67 pi-Stacking: A:F.177, A:F.177 AZA.4: 14 residues within 4Å: Chain A: Y.4, V.63, A.65, T.66, D.67 Chain B: F.177, L.188, R.194, S.241, I.242, Q.243, N.269, Q.297 Ligands: OXY.5 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.194, B:R.194, B:I.242, B:Q.243, B:Q.243, B:N.269, B:Q.297, A:T.66, A:D.67 pi-Stacking: B:F.177, B:F.177 Water bridges: A:K.6 AZA.9: 14 residues within 4Å: Chain C: F.177, L.188, R.194, S.241, I.242, Q.243, N.269, Q.297 Chain D: Y.4, V.63, A.65, T.66, D.67 Ligands: OXY.10 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.194, C:R.194, C:I.242, C:Q.243, C:Q.243, C:N.269, C:Q.297, D:T.66, D:D.67 pi-Stacking: C:F.177, C:F.177 Water bridges: D:K.6 AZA.12: 14 residues within 4Å: Chain C: Y.4, V.63, A.65, T.66, D.67 Chain D: F.177, L.188, R.194, S.241, I.242, Q.243, N.269, Q.297 Ligands: OXY.13 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.194, D:R.194, D:I.242, D:Q.243, D:Q.243, D:N.269, D:Q.297, C:T.66, C:D.67 pi-Stacking: D:F.177, D:F.177

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 7 residues within 4Å: Chain A: I.242, N.269, G.295, Q.297 Chain B: K.6, T.66 Ligands: AZA.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.269, A:G.295, A:Q.297 Water bridges: B:K.6, B:K.6 OXY.5: 6 residues within 4Å: Chain A: T.66 Chain B: I.242, N.269, G.295, Q.297 Ligands: AZA.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.66, B:N.269, B:Q.297 Water bridges: A:K.6 OXY.10: 7 residues within 4Å: Chain C: I.242, N.269, G.295, Q.297 Chain D: K.6, T.66 Ligands: AZA.9 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:N.269, C:G.295, C:Q.297, D:T.66 Water bridges: D:K.6, D:D.67 OXY.13: 7 residues within 4Å: Chain C: K.6, T.66 Chain D: I.242, N.269, G.295, Q.297 Ligands: AZA.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.66, D:N.269, D:Q.297 Water bridges: C:D.67

3 x MXE: 2-METHOXYETHANOL(Non-covalent)

MXE.3: 6 residues within 4Å: Chain A: E.266, Q.268, Y.294, F.296, C.298 Chain B: K.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.43 MXE.7: 6 residues within 4Å: Chain A: K.43 Chain B: E.266, Q.268, Y.294, F.296, C.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 MXE.11: 7 residues within 4Å: Chain C: Y.264, E.266, Q.268, Y.294, F.296, C.298 Chain D: K.43 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.268, C:Y.294

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain B: R.291 Chain D: R.291 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.291, B:R.291 SO4.8: 2 residues within 4Å: Chain A: R.291 Chain C: R.291 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:R.291, A:R.291 Water bridges: A:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibi, T. et al., Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration. To Be Published

Release Date

2018-10-10

Peptides

Uric acid degradation bifunctional protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uric acid degradation bifunctional protein

Related Entries With Identical Sequence