SMTL ID : 4g8j.1

X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine at 2.12 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-hexamer

Ligands

6 x THM: THYMIDINE(Non-covalent)

THM.1: 14 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 Chain B: H.7, R.47 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:H.7, A:T.93, A:Q.165, A:Q.165, A:R.167, A:R.167 Water bridges: B:R.47, B:R.47, A:R.90, A:T.93, A:T.93, A:E.197 Hydrophobic interactions: A:F.161, A:I.219, A:I.220 THM.5: 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: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: 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, A:H.7 Water bridges: B:R.90, B:T.93, B:E.197, B:E.197, A:R.47, A:R.47 THM.8: 15 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 Ligands: EDO.11 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.161, C:I.220 Hydrogen bonds: C:Q.165, C:Q.165, C:R.167, C:R.167, D:H.7 Water bridges: C:R.90, C:T.93, C:E.197, D:R.47, D:R.47, D:R.47 THM.14: 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 15 PLIP interactions: 2 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:H.7, D:T.93, D:Q.165, D:Q.165, D:R.167, D:R.167 Water bridges: C:R.47, D:R.90, D:T.93, D:T.93, D:T.93, D:E.197, D:E.197 Hydrophobic interactions: D:F.161, D:I.220 THM.16: 13 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, I.220 Chain F: H.7, R.47 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:H.7, E:G.95, E:Q.165, E:Q.165, E:R.167, E:R.167 Water bridges: F:R.47, E:E.197 Hydrophobic interactions: E:F.161, E:I.220 THM.20: 14 residues within 4Å: Chain E: H.7, R.47 Chain F: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.219, I.220 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.161, F:I.219, F:I.220 Hydrogen bonds: F:R.90, F:Q.165, F:Q.165, F:R.167, F:R.167, E:H.7 Water bridges: F:T.93, F:T.93

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

CL.2: 4 residues within 4Å: Chain A: V.103, I.220, N.221, K.225 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: P.24, G.25, D.26, R.29, V.91 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: P.24, G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain E: P.24, G.25, D.26 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain F: V.103, I.220, N.221, Q.224, K.225 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain F: P.24, G.25, D.26, R.29 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain F: Y.168, R.174, V.175, Q.180 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: F.171 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain F: F.171 No protein-ligand interaction detected (PLIP)

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

NA.7: 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 A, 3 interactions with chain B Hydrogen bonds: A:I.68, A:S.72, A:S.72, B:I.68, B:S.72 Water bridges: B:S.72 NA.13: 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:E.48, D:I.68, D:S.72, C:E.48, C:I.68, C:S.72 Water bridges: C:S.72 NA.19: 6 residues within 4Å: Chain E: E.48, I.68, S.72 Chain F: E.48, I.68, S.72 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:E.48, F:I.68, F:S.72, E:E.48, E:I.68, E:I.68, E:S.72 Water bridges: E:S.72

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

EDO.9: 5 residues within 4Å: Chain C: Y.162, R.167, D.169 Chain D: F.6, Q.82 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:Q.82, D:Q.82 Water bridges: C:D.169, C:D.169, C:D.169, C:E.226 EDO.10: 3 residues within 4Å: Chain C: R.178 Chain D: L.120, P.124 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain C: F.161 Chain D: H.7 Ligands: THM.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.226, D:H.7 Water bridges: C:T.93 EDO.17: 2 residues within 4Å: Chain E: R.178 Chain F: L.120 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lashkov, A.A. et al., X-ray structure of uridine phosphorylease from Vibrio cholerae complexed with thymidine. To be Published

Release Date

2013-07-24

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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