SMTL ID : 5z2b.1

Crystal structure of highly active BTUO mutant P287G Improved by Humidity Control at 86% RH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

AZA.1: 14 residues within 4Å: Chain A: F.183, L.194, R.200, S.247, I.248, Q.249, N.275, Q.303 Chain B: Y.10, V.69, A.71, T.72, D.73 Ligands: OXY.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.200, A:R.200, A:I.248, A:Q.249, A:Q.249, A:N.275, A:Q.303, B:T.72, B:D.73 pi-Stacking: A:F.183, A:F.183 AZA.5: 14 residues within 4Å: Chain A: Y.10, V.69, A.71, T.72, D.73 Chain B: F.183, L.194, R.200, S.247, I.248, Q.249, N.275, Q.303 Ligands: OXY.4 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.200, B:R.200, B:I.248, B:Q.249, B:Q.249, B:N.275, B:Q.303, A:T.72, A:D.73 pi-Stacking: B:F.183, B:F.183 AZA.10: 14 residues within 4Å: Chain C: F.183, L.194, R.200, S.247, I.248, Q.249, N.275, Q.303 Chain D: Y.10, V.69, A.71, T.72, D.73 Ligands: OXY.12 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.200, C:R.200, C:I.248, C:Q.249, C:Q.249, C:N.275, C:Q.303, D:T.72, D:D.73 pi-Stacking: C:F.183, C:F.183 AZA.14: 14 residues within 4Å: Chain C: Y.10, V.69, A.71, T.72, D.73 Chain D: F.183, L.194, R.200, S.247, I.248, Q.249, N.275, Q.303 Ligands: OXY.13 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.200, D:R.200, D:I.248, D:Q.249, D:Q.249, D:N.275, D:Q.303, C:T.72, C:D.73 pi-Stacking: D:F.183, D:F.183

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

SO4.2: 2 residues within 4Å: Chain A: R.297 Chain D: R.297 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Salt bridges: A:R.297, D:R.297 SO4.11: 2 residues within 4Å: Chain B: R.297 Chain C: R.297 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.297, C:R.297

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 6 residues within 4Å: Chain A: I.248, N.275, G.301, Q.303 Chain B: T.72 Ligands: AZA.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.275, A:Q.303, B:T.72 Water bridges: B:D.73 OXY.4: 6 residues within 4Å: Chain A: T.72 Chain B: I.248, N.275, G.301, Q.303 Ligands: AZA.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.275, B:G.301, B:Q.303, A:T.72 Water bridges: A:K.12, A:D.73 OXY.12: 6 residues within 4Å: Chain C: I.248, N.275, G.301, Q.303 Chain D: T.72 Ligands: AZA.10 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.275, C:Q.303, D:T.72 Water bridges: D:D.73 OXY.13: 6 residues within 4Å: Chain C: T.72 Chain D: I.248, N.275, G.301, Q.303 Ligands: AZA.14 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.275, D:G.301, D:Q.303, C:T.72 Water bridges: C:K.12, C:D.73

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain B: R.132 Chain D: T.30, I.31, P.32, S.34, P.35 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: T.30, I.31, P.32, S.34, P.35 Chain D: R.132 Ligand excluded by PLIP

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

EDO.7: 11 residues within 4Å: Chain B: R.39, E.118, P.120, E.145, Y.146, A.147, L.170, A.229, E.230, R.233 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.230, B:R.233, B:R.233 EDO.8: 7 residues within 4Å: Chain B: D.40, H.41, I.42, L.43, F.121, T.123, F.139 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.41, B:I.42, B:L.43, B:F.121 Water bridges: B:D.40, B:F.121 EDO.9: 9 residues within 4Å: Chain B: P.120, E.122, S.142, N.144, E.145, Y.146, R.233 Chain D: K.140 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.142, B:N.144, B:N.144 Water bridges: B:F.121 EDO.16: 11 residues within 4Å: Chain D: R.39, E.118, P.120, E.145, Y.146, A.147, L.170, A.229, E.230, R.233 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.230, D:R.233, D:R.233 EDO.17: 7 residues within 4Å: Chain D: D.40, H.41, I.42, L.43, F.121, T.123, F.139 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.41, D:I.42, D:L.43, D:F.121 Water bridges: D:D.40, D:F.121 EDO.18: 9 residues within 4Å: Chain B: K.140 Chain D: P.120, E.122, S.142, N.144, E.145, Y.146, R.233 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.142, D:N.144, D:N.144 Water bridges: D:F.121

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

2019-01-02

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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