SMTL ID : 7cuc.1

Crystal Structure of Urate Oxidase from Bacillus sp. TB-90 in the absence from Chloride Anion at 1.44 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 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 11 PLIP interactions: 9 interactions with chain A, 2 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:D.68 pi-Stacking: A:F.178, A:F.178 AZA.10: 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.11 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.195, B:R.195, 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.14: 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.15 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrogen bonds: 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.23: 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.24 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:T.67, C:D.68, D:R.195, D:R.195, D:R.195, D:R.195, D:I.243, D:Q.244, D:Q.244, D:N.270, D:Q.298 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 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.270, A:G.296, A:Q.298, B:T.67 Water bridges: B:K.7 OXY.11: 6 residues within 4Å: Chain A: T.67 Chain B: I.243, N.270, G.296, Q.298 Ligands: AZA.10 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.67, B:N.270, B:G.296, B:Q.298 Water bridges: A:K.7 OXY.15: 6 residues within 4Å: Chain C: I.243, N.270, G.296, Q.298 Chain D: T.67 Ligands: AZA.14 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:T.67, C:N.270, C:G.296, C:Q.298 Water bridges: D:K.7 OXY.24: 6 residues within 4Å: Chain C: T.67 Chain D: I.243, N.270, G.296, Q.298 Ligands: AZA.23 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.67, D:N.270, D:G.296, D:Q.298 Water bridges: C:K.7

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

NA.3: 6 residues within 4Å: Chain A: T.25, I.26, P.27, S.29, P.30 Chain C: R.127 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.25, A:T.25, C:R.127 Water bridges: A:I.26 NA.13: 1 residues within 4Å: Chain B: S.32 3 PLIP interactions: 3 interactions with chain B Water bridges: B:S.32, B:S.32, B:S.32 NA.16: 6 residues within 4Å: Chain A: R.127 Chain C: T.25, I.26, P.27, S.29, P.30 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.25, C:T.25, A:R.127 Water bridges: C:I.26 NA.26: 1 residues within 4Å: Chain D: S.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.32

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

MXE.4: 9 residues within 4Å: Chain A: E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.113, A:R.228 Water bridges: A:R.34, A:F.116 MXE.5: 7 residues within 4Å: Chain A: Y.4, S.46, V.47, G.48, K.106, I.107, S.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.106 MXE.6: 8 residues within 4Å: Chain A: D.35, H.36, I.37, L.38, F.116, E.117, T.118, F.134 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.36, A:I.37, A:L.38 Water bridges: A:D.35, A:D.35, A:D.35 MXE.7: 7 residues within 4Å: Chain A: Y.4, K.44 Chain B: E.267, Q.269, Y.295, F.297, C.299 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.44, B:Q.269, B:Y.295 MXE.8: 9 residues within 4Å: Chain A: E.267, Q.269, Y.295, F.297, C.299 Chain B: Y.4, K.44, S.46 Ligands: MXE.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.269, A:Y.295, B:K.44 MXE.9: 10 residues within 4Å: Chain A: F.297 Chain B: Y.4, K.44, I.45, S.46, S.108, L.109, I.110, Y.145 Ligands: MXE.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.4, B:S.46 MXE.17: 9 residues within 4Å: Chain C: E.113, P.115, E.140, Y.141, A.142, L.165, A.224, E.225, R.228 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.113, C:R.228 Water bridges: C:R.34, C:F.116 MXE.18: 7 residues within 4Å: Chain C: Y.4, S.46, V.47, G.48, K.106, I.107, S.108 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.106 MXE.19: 8 residues within 4Å: Chain C: D.35, H.36, I.37, L.38, F.116, E.117, T.118, F.134 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.36, C:I.37, C:L.38 Water bridges: C:D.35, C:D.35, C:D.35 MXE.20: 7 residues within 4Å: Chain C: Y.4, K.44 Chain D: E.267, Q.269, Y.295, F.297, C.299 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.44, D:Q.269, D:Y.295 MXE.21: 9 residues within 4Å: Chain C: E.267, Q.269, Y.295, F.297, C.299 Chain D: Y.4, K.44, S.46 Ligands: MXE.22 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.44, C:Q.269, C:Y.295 MXE.22: 10 residues within 4Å: Chain C: F.297 Chain D: Y.4, K.44, I.45, S.46, S.108, L.109, I.110, Y.145 Ligands: MXE.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.4, D:S.46

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

SO4.12: 2 residues within 4Å: Chain B: R.292 Chain C: R.292 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:R.292, B:R.292 Salt bridges: C:R.292, B:R.292 SO4.25: 2 residues within 4Å: Chain A: R.292 Chain D: R.292 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Water bridges: A:R.292, D:R.292 Salt bridges: A:R.292, D:R.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibi, T. et al., Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J.Biochem. (2021)

Release Date

2020-11-25

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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