SMTL ID : 5our.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 2,2'-anhydrouridine at 1.34 A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-hexamer

Ligands

3 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 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.68, A:I.68, A:S.72, B:E.48, B:I.68, B:S.72 Water bridges: A:S.72 NA.10: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.48, D:E.48, D:I.68, D:S.72, C:I.68, C:S.72 Water bridges: D: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: 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:E.48, F:I.68, F:S.72, E:I.68, E:I.68, E:S.72 Water bridges: E:S.72

6 x BJE: 2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil(Non-covalent)

BJE.2: 12 residues within 4Å: Chain A: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 Chain B: H.7, R.47 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:H.7, B:R.47, A:G.95, A:Q.165, A:E.197 Water bridges: B:R.47, B:R.47, A:R.90, A:R.90, A:T.93, A:T.93, A:R.167, A:R.167 BJE.4: 12 residues within 4Å: Chain A: H.7, R.47 Chain B: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.93, B:G.95, B:Q.165, B:E.197, A:H.7, A:R.47 Water bridges: B:R.90, B:R.90, B:T.93, B:R.167, B:R.167, A:R.47, A:R.47 BJE.9: 12 residues within 4Å: Chain C: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 Chain D: H.7, R.47 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:H.7, D:R.47, C:G.95, C:Q.165, C:E.197 Water bridges: D:R.47, D:R.47, C:R.90, C:R.90, C:T.93, C:R.167 BJE.11: 12 residues within 4Å: Chain C: H.7, R.47 Chain D: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:T.93, D:G.95, D:Q.165, D:E.197, C:H.7, C:R.47 Water bridges: D:R.90, D:R.90, D:T.93, D:R.167, D:R.167, C:R.47, C:R.47 BJE.16: 12 residues within 4Å: Chain E: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 Chain F: H.7, R.47 12 PLIP interactions: 4 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:H.7, F:R.47, E:G.95, E:Q.165, E:E.197 Water bridges: F:R.47, F:R.47, E:R.90, E:R.90, E:T.93, E:R.167, E:R.167 BJE.18: 12 residues within 4Å: Chain E: H.7, R.47 Chain F: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:H.7, E:R.47, F:T.93, F:G.95, F:Q.165, F:M.196, F:E.197 Water bridges: E:R.47, E:R.47, F:R.90, F:R.90, F:T.93, F:R.167

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

CL.3: 2 residues within 4Å: Chain B: D.38, N.39 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: D.132, F.133 Chain C: T.110, M.152 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: T.110, M.152 Chain C: D.132, F.133 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: T.110, M.152 Chain F: D.132, F.133 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain B: F.6, H.7, G.9, H.46 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.7 Water bridges: B:G.9 EDO.12: 4 residues within 4Å: Chain C: Q.82 Chain D: D.169, T.170, F.171 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:A.81, C:Q.82 Hydrogen bonds: D:D.169 EDO.19: 2 residues within 4Å: Chain A: M.125 Chain F: M.125 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain B: L.115, R.178, F.179, E.185, W.186 Chain C: P.124, E.126 Chain D: R.177 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.178, B:E.185, C:E.126 GOL.13: 6 residues within 4Å: Chain D: L.115, R.178, F.179, E.185 Chain E: E.126 Chain F: R.177 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:R.178, D:R.178, D:E.185, E:E.126 Water bridges: E:E.126 GOL.14: 3 residues within 4Å: Chain D: P.99, H.100, N.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.100, D:N.102 Water bridges: D:N.102 GOL.20: 7 residues within 4Å: Chain A: P.124, E.126 Chain B: R.177 Chain F: L.115, R.178, F.179, E.185 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: A:E.126, F:R.178, F:E.185 Water bridges: B:R.177 GOL.21: 3 residues within 4Å: Chain F: K.184, Q.187, D.188 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.184, F:Q.187 Water bridges: F:Q.187, F:Q.187, F:D.188 GOL.22: 4 residues within 4Å: Chain E: D.169, T.170, F.171 Chain F: Q.82 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:D.169, F:Q.82 Water bridges: E:T.170

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

MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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 2,2'-anhydrouridine at 1.34 A. To Be Published

Release Date

2018-09-05

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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