SMTL ID : 5m2t.1

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-hexamer

Ligands

6 x URI: URIDINE(Non-covalent)

URI.1: 19 residues within 4Å: Chain A: I.68, G.69, 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 Chain B: F.6, H.7, R.47, I.75 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.165, A:Q.165, A:R.167, A:M.196, A:E.197, A:E.197, B:H.7 Water bridges: A:R.90, A:R.90, A:R.167, A:R.167, B:R.47, B:R.47, B:R.47 URI.3: 21 residues within 4Å: Chain A: F.6, H.7, R.47, I.75 Chain B: I.68, G.69, 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, R.222, P.228 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.219 Hydrogen bonds: B:R.90, B:Q.165, B:Q.165, B:R.167, B:R.167, B:M.196, B:E.197, B:E.197, A:H.7 Water bridges: B:T.93, A:R.47, A:R.47, A:R.47 URI.5: 19 residues within 4Å: Chain C: I.68, G.69, 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 Chain D: F.6, H.7, R.47, I.75 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.165, C:Q.165, C:R.167, C:M.196, C:E.197, C:E.197, D:H.7 Water bridges: C:T.93, C:E.195, D:R.47, D:R.47 URI.9: 19 residues within 4Å: Chain C: F.6, H.7, R.47, I.75 Chain D: I.68, G.69, 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 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.95, D:Q.165, D:Q.165, D:R.167, D:M.196, D:E.197, D:E.197, C:H.7 Water bridges: D:R.90, D:R.90, D:R.167, D:R.167, D:E.197, C:R.47 URI.13: 21 residues within 4Å: Chain E: I.68, G.69, 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 Chain F: F.6, H.7, R.47, I.75 Ligands: EDO.15 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:H.7, E:Q.165, E:Q.165, E:R.167, E:R.167, E:M.196, E:E.197, E:E.197 Water bridges: F:R.47, F:R.47, E:R.90 URI.16: 19 residues within 4Å: Chain E: F.6, H.7, R.47, I.75 Chain F: I.68, G.69, 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 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:H.7, F:Q.165, F:Q.165, F:R.167, F:M.196, F:E.197, F:E.197 Water bridges: E:R.47, E:R.47, F:R.90, F:R.90, F:R.90, F:R.90, F:R.167, F:R.167

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

NA.2: 8 residues within 4Å: Chain A: E.48, G.67, I.68, S.72 Chain B: E.48, G.67, I.68, S.72 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.48, B:I.68, A:E.48, A:I.68, A:I.68 Water bridges: A:S.72 NA.8: 8 residues within 4Å: Chain C: E.48, G.67, I.68, S.72 Chain D: E.48, G.67, I.68, S.72 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.68, D:S.72, C:I.68, C:S.72 Water bridges: D:S.72 NA.14: 8 residues within 4Å: Chain E: E.48, G.67, I.68, S.72 Chain F: E.48, G.67, I.68, S.72 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:E.48, E:I.68, F:E.48, F:I.68 Water bridges: E:S.72

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

CL.4: 7 residues within 4Å: Chain A: R.47 Chain B: P.24, G.25, D.26, R.29, G.92, T.93 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: T.110, M.152, G.153 Chain C: D.132, F.133 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain D: D.132, F.133 Chain E: T.110, M.152, G.153 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain C: R.47 Chain D: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain E: R.47 Chain F: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.12: 1 residues within 4Å: Chain D: A.206 No protein-ligand interaction detected (PLIP)

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

EDO.15: 9 residues within 4Å: Chain E: G.25, R.90, V.91, G.92, T.93, E.195, E.197 Chain F: R.47 Ligands: URI.13 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.90, E:T.93, E:E.197, F:R.47, F:R.47 Water bridges: E:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution. To Be Published

Release Date

2017-11-15

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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