SMTL ID : 4ogl.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-hexamer

Ligands

6 x TDR: THYMINE(Non-covalent)

TDR.1: 13 residues within 4Å: Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, P.228 Ligands: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.219, A:I.220, A:P.228 Hydrogen bonds: A:Q.165, A:Q.165, A:R.167, A:R.167 TDR.5: 11 residues within 4Å: Chain B: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.220 Ligands: TRS.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.220 Hydrogen bonds: B:T.93, B:Q.165, B:Q.165, B:R.167, B:R.167 Water bridges: B:G.95, B:G.95 TDR.8: 12 residues within 4Å: Chain C: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.219, C:I.220 Hydrogen bonds: C:T.93, C:Q.165, C:Q.165, C:R.167, C:R.167 Water bridges: C:M.196 TDR.14: 13 residues within 4Å: Chain D: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.15, GOL.16 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.219, D:I.220 Hydrogen bonds: D:T.93, D:Q.165, D:Q.165, D:R.167, D:R.167 Water bridges: D:M.196, D:M.196 TDR.17: 10 residues within 4Å: Chain E: T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.220 Ligands: GOL.20 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:I.220 Hydrogen bonds: E:G.95, E:Q.165, E:Q.165, E:R.167, E:R.167 TDR.22: 13 residues within 4Å: Chain F: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, P.228 Ligands: GOL.25 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.161, F:I.219, F:I.220, F:P.228 Hydrogen bonds: F:T.93, F:Q.165, F:Q.165, F:R.167, F:R.167 Water bridges: F:M.196, F:M.196

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

EDO.2: 2 residues within 4Å: Chain A: R.178 Chain B: L.120 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.178 EDO.6: 5 residues within 4Å: Chain B: T.4, F.6, H.7, G.9, H.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.7 EDO.9: 2 residues within 4Å: Chain C: R.178 Chain D: L.120 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Water bridges: C:R.178, D:A.123, B:E.126 EDO.10: 2 residues within 4Å: Chain C: D.132, A.206 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:V.154, C:F.133 Hydrogen bonds: C:D.132, C:D.132 EDO.11: 5 residues within 4Å: Chain C: K.3, Q.82 Chain D: D.169, T.170, F.171 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.169, C:K.3 Water bridges: D:F.171 EDO.18: 2 residues within 4Å: Chain D: M.125 Chain E: M.125 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.126, E:E.126 EDO.19: 2 residues within 4Å: Chain E: R.178 Chain F: L.120 1 PLIP interactions: 1 interactions with chain E Water bridges: E:R.178 EDO.23: 4 residues within 4Å: Chain F: G.17, T.19, Q.59, S.60 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.60, F:S.60 Water bridges: F:T.19, F:T.19, F:Q.59, F:Q.59 EDO.24: 3 residues within 4Å: Chain A: M.125 Chain F: M.125, E.126 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:E.126, A:E.126

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: I.68, T.93, F.161, M.196, E.197 Chain B: H.7 Ligands: TDR.1 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.7, B:R.47, A:R.90, A:T.93, A:T.93, A:E.197 Water bridges: B:R.47, B:R.47, B:R.47, A:T.93, A:T.93 GOL.12: 7 residues within 4Å: Chain C: I.68, T.93, F.161, M.196, E.197 Chain D: H.7 Ligands: TDR.8 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.93, C:E.197, D:H.7, D:R.47 Water bridges: C:R.90, C:T.93 GOL.15: 8 residues within 4Å: Chain C: H.7, R.47 Chain D: I.68, F.161, M.196, E.197 Ligands: TDR.14, GOL.16 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:H.7, C:R.47, D:E.197 Water bridges: D:T.93, D:T.93, D:T.93, D:T.93, D:E.197 GOL.16: 5 residues within 4Å: Chain C: F.6 Chain D: F.161, E.226 Ligands: TDR.14, GOL.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:F.6, D:E.226 GOL.20: 8 residues within 4Å: Chain E: I.68, T.93, F.161, M.196, E.197 Chain F: H.7, R.47 Ligands: TDR.17 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:H.7, F:R.47, E:T.93, E:T.93, E:E.197 Water bridges: F:R.47, F:R.47, E:T.93 GOL.25: 8 residues within 4Å: Chain E: H.7 Chain F: I.68, R.90, T.93, F.161, M.196, E.197 Ligands: TDR.22 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.90, F:T.93, F:E.197, E:H.7 Water bridges: F:T.93, F:T.93, F:T.93

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

NA.4: 6 residues within 4Å: Chain A: E.48, I.68, S.72 Chain B: E.48, I.68, S.72 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.48, B:I.68, B:S.72, A:I.68, A:S.72 Water bridges: A:S.72 NA.13: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.48, D:I.68, D:S.72, C:E.48, C:I.68, C:I.68, C:S.72 Water bridges: D:S.72 NA.21: 6 residues within 4Å: Chain E: E.48, I.68, S.72 Chain F: E.48, I.68, S.72 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:E.48, F:E.48, F:I.68, F:S.72, E:I.68, E:S.72 Water bridges: E:S.72

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 9 residues within 4Å: Chain A: H.7, R.47 Chain B: I.68, T.93, F.161, E.195, M.196, E.197 Ligands: TDR.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.93, B:T.93, B:M.196, B:E.197, A:H.7, A:R.47 Water bridges: B:R.90, B:R.90, B:T.93, B:T.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution. Crystallogr. Rep. (2016)

Release Date

2015-03-04

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase

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