SMTL ID : 4ip0.1

X-Ray Structure of the Complex Uridine Phosphorylase from Vibrio cholerae with Phosphate Ion at 1.29 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 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:E.48, A:I.68, A:S.72, B:I.68, B:S.72 Water bridges: A:S.72 NA.15: 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:I.68, F:I.68, F:S.72, E:I.68, E:S.72 Water bridges: E:S.72

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

EDO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: G.92, T.93 Chain B: R.47 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.93, A:T.93, B:R.47, B:R.47 Water bridges: A:E.197, A:E.197 EDO.11: 9 residues within 4Å: Chain C: T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196 Ligands: CL.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.95, C:Q.165 Water bridges: C:T.93, C:T.93, C:E.197 EDO.12: 2 residues within 4Å: Chain C: R.239, K.242 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.239, C:K.242, C:K.242 EDO.18: 4 residues within 4Å: Chain E: E.166, Y.168, M.183, R.222 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.166, E:R.222, E:R.222 EDO.22: 9 residues within 4Å: Chain F: T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196 Ligands: CL.21 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.95, F:Q.165 Water bridges: F:T.93, F:T.93, F:E.197 EDO.23: 7 residues within 4Å: Chain A: S.207, S.208, G.209 Chain B: R.174 Chain F: D.188, M.189, G.190 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: B:R.174, F:M.189 Water bridges: B:R.174, A:G.209

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 1 residues within 4Å: Chain B: R.86 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.86 Salt bridges: B:R.86 PO4.4: 7 residues within 4Å: Chain A: R.47 Chain B: G.25, R.29, R.90, V.91, G.92, T.93 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain B Salt bridges: A:R.47, B:R.29, B:R.90 Hydrogen bonds: B:G.25, B:D.26, B:T.93, B:T.93 Water bridges: B:R.90, B:R.90, B:T.93, B:T.93, B:E.195, B:E.197, B:E.197 PO4.9: 9 residues within 4Å: Chain C: P.24, G.25, D.26, R.29, R.90, V.91, G.92, T.93 Chain D: R.47 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.25, C:D.26, C:T.93, C:T.93 Water bridges: C:T.66, C:R.90, C:R.90, C:R.90 Salt bridges: C:R.29, C:R.90, D:R.47 PO4.19: 9 residues within 4Å: Chain E: R.47 Chain F: P.24, G.25, D.26, R.29, R.90, V.91, G.92, T.93 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.25, F:D.26, F:T.93, F:T.93, F:T.93 Water bridges: F:T.66, F:R.90, F:R.90, F:R.90 Salt bridges: F:R.29, F:R.90, E:R.47 PO4.20: 2 residues within 4Å: Chain F: K.140, Q.144 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Q.144, F:Q.144 Water bridges: F:K.140, F:K.140, F:K.140, F:K.140 Salt bridges: F:K.140

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

SO4.5: 2 residues within 4Å: Chain B: K.140, Q.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.144 Water bridges: B:K.140, B:K.140 Salt bridges: B:K.140 SO4.6: 3 residues within 4Å: Chain B: R.177 Chain D: R.177 Chain F: R.177 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F, 3 interactions with chain D Water bridges: B:R.177, D:R.177, D:R.177 Salt bridges: B:R.177, F:R.177, D:R.177 SO4.14: 2 residues within 4Å: Chain C: A.28 Chain D: H.46 4 PLIP interactions: 4 interactions with chain D Water bridges: D:S.45, D:H.46, D:R.47 Salt bridges: D:H.46 SO4.16: 3 residues within 4Å: Chain E: G.92, T.93 Chain F: R.47 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.93 Water bridges: E:G.25, E:G.25, F:R.47, F:R.47 Salt bridges: F:R.47 SO4.17: 1 residues within 4Å: Chain E: R.86 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.86 Salt bridges: E:R.86

1 x EOH: ETHANOL(Non-functional Binders)

EOH.8: 2 residues within 4Å: Chain B: G.209 Chain C: G.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.206 Water bridges: B:G.209

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

CL.10: 5 residues within 4Å: Chain C: G.95, F.161, R.167, I.220 Ligands: EDO.11 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain F: G.95, F.161, Q.165, R.167, I.220 Ligands: EDO.22 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.13: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.48

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

2014-08-13

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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