SMTL ID : 5y2p.1

Crystal Structure of Bacillus sp. TB-90 Urate Oxidase Improved by Humidity Control at 89% RH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.6: 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.7 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.66, A:D.67, B:R.194, B:R.194, B:I.242, B:Q.243, B:Q.243, B:N.269, B:Q.297 Water bridges: A:K.6, A:T.66 pi-Stacking: B:F.177, B:F.177 AZA.13: 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.14 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:T.66, D:D.67 pi-Stacking: C:F.177, C:F.177 AZA.18: 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.19 13 PLIP interactions: 9 interactions with chain D, 4 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 Water bridges: C:K.6, C:T.66

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:D.67 OXY.7: 7 residues within 4Å: Chain A: K.6, T.66 Chain B: I.242, N.269, G.295, Q.297 Ligands: AZA.6 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.269, B:G.295, B:Q.297, A:T.66 Water bridges: A:K.6, A:K.6, A:K.6 OXY.14: 7 residues within 4Å: Chain C: I.242, N.269, G.295, Q.297 Chain D: K.6, T.66 Ligands: AZA.13 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Water bridges: D:K.6, D:D.67 Hydrogen bonds: C:N.269, C:G.295, C:Q.297 OXY.19: 7 residues within 4Å: Chain C: K.6, T.66 Chain D: I.242, N.269, G.295, Q.297 Ligands: AZA.18 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.269, D:G.295, D:Q.297, C:T.66 Water bridges: C:K.6, C:K.6, C:K.6

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

SO4.3: 2 residues within 4Å: Chain A: R.291 Chain D: R.291 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Salt bridges: D:R.291, A:R.291 SO4.15: 2 residues within 4Å: Chain B: R.291 Chain C: R.291 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:R.291, B:R.291

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

EDO.4: 6 residues within 4Å: Chain A: D.34, H.35, I.36, L.37, F.115, F.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.35, A:I.36, A:L.37, A:F.115 Water bridges: A:D.34, A:F.115 EDO.5: 8 residues within 4Å: Chain A: E.112, E.139, Y.140, A.141, L.164, A.223, E.224, R.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.141, A:E.224, A:R.227, A:R.227 EDO.9: 11 residues within 4Å: Chain B: R.33, E.112, P.114, E.139, Y.140, A.141, L.164, A.223, E.224, R.227 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.141, B:E.224, B:R.227, B:R.227 EDO.10: 9 residues within 4Å: Chain B: P.114, F.115, E.116, S.136, N.138, E.139, R.227 Chain D: K.134 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.136, B:N.138 Water bridges: B:F.115, B:F.115 EDO.11: 7 residues within 4Å: Chain B: D.34, H.35, I.36, L.37, F.115, T.117, F.133 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.35, B:I.36, B:L.37, B:F.115 Water bridges: B:D.34, B:F.115 EDO.12: 8 residues within 4Å: Chain B: R.33, H.35, F.38, G.39, T.84, I.85, E.112, P.114 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.33, B:E.112 Water bridges: B:L.37, B:L.37, B:G.39, B:F.115 EDO.16: 6 residues within 4Å: Chain C: D.34, H.35, I.36, L.37, F.115, F.133 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.35, C:I.36, C:L.37, C:F.115 Water bridges: C:D.34, C:F.115 EDO.17: 8 residues within 4Å: Chain C: E.112, E.139, Y.140, A.141, L.164, A.223, E.224, R.227 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.141, C:E.224, C:R.227, C:R.227 EDO.21: 11 residues within 4Å: Chain D: R.33, E.112, P.114, E.139, Y.140, A.141, L.164, A.223, E.224, R.227 Ligands: EDO.22 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.141, D:E.224, D:R.227, D:R.227 EDO.22: 9 residues within 4Å: Chain B: K.134 Chain D: P.114, F.115, E.116, S.136, N.138, E.139, R.227 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.136, D:N.138 Water bridges: D:F.115, D:F.115 EDO.23: 7 residues within 4Å: Chain D: D.34, H.35, I.36, L.37, F.115, T.117, F.133 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.35, D:I.36, D:L.37, D:F.115 Water bridges: D:D.34, D:F.115 EDO.24: 8 residues within 4Å: Chain D: R.33, H.35, F.38, G.39, T.84, I.85, E.112, P.114 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.33, D:E.112 Water bridges: D:L.37, D:L.37, D:G.39, D:F.115

2 x K: POTASSIUM ION(Non-covalent)

K.8: 6 residues within 4Å: Chain B: T.24, I.25, P.26, S.28, P.29 Chain D: R.126 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.25, B:S.28 K.20: 6 residues within 4Å: Chain B: R.126 Chain D: T.24, I.25, P.26, S.28, P.29 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:I.25, D:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hibi, T. et al., Conformational Flexibility of Plastic Interface Loop Allows Entropic Adaptation of Urate Oxidase to Environmental pH. To Be Published

Release Date

2018-08-08

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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