SMTL ID : 7cmn.1

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 88% RH.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-tetramer

Ligands

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

AZA.1: 14 residues within 4Å: Chain A: F.178, L.189, R.195, S.242, I.243, Q.244, N.270, Q.298 Chain B: Y.5, V.64, A.66, T.67, D.68 Ligands: OXY.2 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.195, A:R.195, A:I.243, A:Q.244, A:Q.244, A:N.270, A:Q.298, B:T.67, B:T.67, B:D.68 pi-Stacking: A:F.178, A:F.178 AZA.5: 14 residues within 4Å: Chain A: Y.5, V.64, A.66, T.67, D.68 Chain B: F.178, L.189, R.195, S.242, I.243, Q.244, N.270, Q.298 Ligands: OXY.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.195, B:R.195, B:I.243, B:Q.244, B:Q.244, B:N.270, B:Q.298, A:T.67, A:D.68 pi-Stacking: B:F.178, B:F.178 AZA.12: 14 residues within 4Å: Chain C: F.178, L.189, R.195, S.242, I.243, Q.244, N.270, Q.298 Chain D: Y.5, V.64, A.66, T.67, D.68 Ligands: OXY.13 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:T.67, D:T.67, D:D.68, C:R.195, C:R.195, C:I.243, C:Q.244, C:Q.244, C:N.270, C:Q.298 pi-Stacking: C:F.178, C:F.178 AZA.16: 14 residues within 4Å: Chain C: Y.5, V.64, A.66, T.67, D.68 Chain D: F.178, L.189, R.195, S.242, I.243, Q.244, N.270, Q.298 Ligands: OXY.17 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.195, D:R.195, D:I.243, D:Q.244, D:Q.244, D:N.270, D:Q.298, C:T.67, C:D.68 pi-Stacking: D:F.178, D:F.178

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 6 residues within 4Å: Chain A: I.243, N.270, G.296, Q.298 Chain B: T.67 Ligands: AZA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.270, A:Q.298 OXY.6: 6 residues within 4Å: Chain A: T.67 Chain B: I.243, N.270, G.296, Q.298 Ligands: AZA.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.270, B:G.296, B:Q.298, A:T.67 OXY.13: 6 residues within 4Å: Chain C: I.243, N.270, G.296, Q.298 Chain D: T.67 Ligands: AZA.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.270, C:Q.298 OXY.17: 6 residues within 4Å: Chain C: T.67 Chain D: I.243, N.270, G.296, Q.298 Ligands: AZA.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.270, D:G.296, D:Q.298, C:T.67

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

SO4.3: 2 residues within 4Å: Chain A: R.292 Chain D: R.292 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Water bridges: D:R.292 Salt bridges: D:R.292, A:R.292 SO4.14: 2 residues within 4Å: Chain B: R.292 Chain C: R.292 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.292, B:R.292 Water bridges: B:R.292

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 10 residues within 4Å: Chain A: R.34, E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.142, A:E.225 EDO.7: 6 residues within 4Å: Chain B: D.35, H.36, I.37, L.38, F.116, F.134 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.36, B:I.37, B:L.38, B:F.116 Water bridges: B:D.35, B:F.116 EDO.8: 9 residues within 4Å: Chain B: P.115, F.116, E.117, S.137, N.139, E.140, R.228 Chain D: K.135 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.137, B:N.139, B:N.139 Water bridges: B:F.116, B:F.116 EDO.9: 12 residues within 4Å: Chain B: R.34, E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 Ligands: EDO.8, EDO.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.142, B:E.225, B:R.228, B:R.228 EDO.10: 8 residues within 4Å: Chain B: R.34, H.36, F.39, G.40, I.86, E.113, A.142 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.113 Water bridges: B:R.34, B:R.34, B:G.40, B:E.113, B:I.114 EDO.11: 4 residues within 4Å: Chain B: Y.200, Q.269, H.271, Y.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.269, B:H.271 EDO.15: 10 residues within 4Å: Chain C: R.34, E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.142, C:E.225 EDO.18: 6 residues within 4Å: Chain D: D.35, H.36, I.37, L.38, F.116, F.134 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.36, D:I.37, D:L.38, D:F.116 Water bridges: D:D.35, D:F.116 EDO.19: 9 residues within 4Å: Chain B: K.135 Chain D: P.115, F.116, E.117, S.137, N.139, E.140, R.228 Ligands: EDO.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.137, D:N.139, D:N.139 Water bridges: D:F.116, D:F.116 EDO.20: 12 residues within 4Å: Chain D: R.34, E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 Ligands: EDO.19, EDO.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.142, D:E.225, D:R.228, D:R.228 EDO.21: 8 residues within 4Å: Chain D: R.34, H.36, F.39, G.40, I.86, E.113, A.142 Ligands: EDO.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.113 Water bridges: D:R.34, D:R.34, D:G.40, D:E.113, D:I.114 EDO.22: 4 residues within 4Å: Chain D: Y.200, Q.269, H.271, Y.295 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.269, D:H.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibi, T. et al., Flexibility of a Distal Interface Loop Modulates Water Network in the Active Site of Bacillus sp. TB-90 Urate Oxidase. To be published

Release Date

2020-08-12

Peptides

Uric acid degradation bifunctional protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Uric acid degradation bifunctional protein

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