SMTL ID : 4lzw.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymidine at 1.29 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-hexamer

Ligands

6 x THM: THYMIDINE(Non-covalent)

THM.1: 15 residues within 4Å: Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, P.228 Chain B: H.7, R.47 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.161, A:M.196, A:I.219, A:I.220, A:P.228 Hydrogen bonds: A:R.90, A:T.93, A:Q.165, A:Q.165, A:R.167, A:R.167, B:H.7 Water bridges: A:T.93, A:T.93, A:E.197, B:R.47, B:R.47 THM.8: 15 residues within 4Å: Chain A: H.7, R.47 Chain B: I.68, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.161, B:F.161, B:I.219, B:I.220 Hydrogen bonds: B:T.93, B:Q.165, B:Q.165, B:R.167, B:R.167 Water bridges: B:T.93, B:T.93, B:E.197, B:E.197, A:R.47, A:R.47 THM.13: 14 residues within 4Å: Chain C: I.68, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.220 Chain D: H.7, R.47 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.161, C:I.220 Hydrogen bonds: C:T.93, C:Q.165, C:Q.165, C:R.167, C:R.167, D:H.7 Water bridges: C:R.90, C:R.90, C:T.93, C:E.197, D:R.47 THM.19: 14 residues within 4Å: Chain C: H.7, R.47 Chain D: I.68, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.220 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.161, D:F.161, D:I.220 Hydrogen bonds: D:T.93, D:Q.165, D:Q.165, D:R.167, D:R.167, C:H.7 Water bridges: D:R.90, D:T.93, D:T.93, D:E.197, D:E.197 THM.24: 12 residues within 4Å: Chain E: I.68, T.93, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197 Chain F: H.7, R.47 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:F.161 Hydrogen bonds: E:Q.165, E:Q.165, E:R.167, E:R.167, F:H.7, F:R.47 Water bridges: E:R.90, E:T.93, E:E.197, E:E.197, F:R.47 THM.29: 16 residues within 4Å: Chain E: H.7, R.47 Chain F: R.90, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220, P.228 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:F.161, F:M.196, F:I.219, F:I.220, F:P.228 Hydrogen bonds: F:R.90, F:Q.165, F:Q.165, F:R.167, F:R.167, E:H.7, E:R.47 Water bridges: F:T.93, F:T.93, F:E.197, F:E.197, E:R.47

7 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 2 residues within 4Å: Chain A: R.178 Chain B: L.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.178 EOH.3: 3 residues within 4Å: Chain A: M.125, E.126 Chain F: M.125 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.126 Hydrophobic interactions: F:M.125 EOH.9: 2 residues within 4Å: Chain B: M.125 Chain C: M.125 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.126, C:E.126 EOH.10: 2 residues within 4Å: Chain A: L.120 Chain B: R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.178 EOH.20: 2 residues within 4Å: Chain C: L.120 Chain D: R.178 No protein-ligand interaction detected (PLIP) EOH.26: 2 residues within 4Å: Chain E: R.178 Chain F: L.120 No protein-ligand interaction detected (PLIP) EOH.30: 2 residues within 4Å: Chain E: L.120 Chain F: R.178 No protein-ligand interaction detected (PLIP)

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

CL.4: 4 residues within 4Å: Chain A: P.24, G.25, D.26, R.29 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: V.103, I.220, N.221, Q.224, K.225 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain E: P.24, G.25, D.26 Chain F: R.47 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain F: P.24, G.25, D.26, R.29 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain F: V.103, I.220, N.221, Q.224, K.225 Ligand excluded by PLIP

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

NA.5: 6 residues within 4Å: Chain A: E.48, I.68, S.72 Chain B: E.48, I.68, S.72 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.68, A:I.68, A:S.72, B:I.68, B:S.72 Water bridges: A:S.72 NA.16: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:I.68, D:S.72, C:E.48, C:I.68, C:S.72, C:S.72 Water bridges: D:S.72 NA.32: 7 residues within 4Å: Chain E: E.48, I.68, S.72 Chain F: E.48, G.67, I.68, S.72 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:E.48, E:I.68, E:S.72, F:E.48, F:I.68, F:I.68, F:S.72 Water bridges: E:S.72

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 1 residues within 4Å: Chain A: Q.180 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: Q.180 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: MG.18 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain C: N.102 Ligands: MG.17 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: MG.23 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain D: N.102 Ligands: MG.22 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain E: Q.180 No protein-ligand interaction detected (PLIP)

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

EDO.14: 2 residues within 4Å: Chain C: R.178 Chain D: L.120 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Water bridges: C:R.178, B:E.126, D:A.123 EDO.25: 2 residues within 4Å: Chain E: M.183, Q.187 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.187, E:Q.187 Water bridges: E:E.166, E:G.181, E:M.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases. Crystallography Reports (2016)

Release Date

2014-12-31

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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