SMTL ID : 5c80.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-hexamer

Ligands

6 x URI: URIDINE(Non-covalent)

URI.1: 13 residues within 4Å: Chain A: 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 B: H.7 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:H.7, A:R.90, A:T.93, A:T.93, A:Q.165, A:Q.165, A:R.167, A:R.167, A:M.196, A:E.197 Water bridges: B:R.47, B:R.47, A:T.93 URI.6: 16 residues within 4Å: Chain A: H.7, R.47 Chain B: I.68, 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: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.219 Hydrogen bonds: B:R.90, B:T.93, B:T.93, B:Q.165, B:Q.165, B:R.167, B:R.167, B:M.196, B:E.197, A:H.7 Water bridges: B:R.90, B:R.90, A:R.47, A:R.47 URI.12: 13 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 Chain D: H.7, R.47 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.93, C:Q.165, C:Q.165, C:R.167, C:R.167, C:M.196, C:E.197, D:H.7, D:R.47 Water bridges: C:R.90, C:R.90, C:T.93 URI.16: 13 residues within 4Å: Chain C: H.7 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 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.90, D:T.93, D:T.93, D:Q.165, D:Q.165, D:R.167, D:M.196, D:E.197, C:H.7 Water bridges: D:T.93, D:R.167, D:R.167 URI.21: 15 residues within 4Å: Chain E: 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 Chain F: H.7, R.47 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:I.219 Hydrogen bonds: E:R.90, E:T.93, E:Q.165, E:Q.165, E:R.167, E:R.167, E:M.196, E:E.197, F:H.7 Water bridges: F:R.47, F:R.47 URI.23: 14 residues within 4Å: Chain E: H.7, R.47 Chain F: I.68, T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, E.197, I.220 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:T.93, F:Q.165, F:Q.165, F:R.167, F:R.167, F:M.196, F:E.197, E:H.7 Water bridges: F:R.90, F:T.93, E:R.47, E:R.47

9 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: D.132, A.206, L.210 Chain F: M.152, G.153 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:P.131, A:A.206, F:M.152 Water bridges: A:D.132, A:G.209, F:V.154 TRS.7: 5 residues within 4Å: Chain B: P.131, D.132, A.206, L.210 Chain C: M.152 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.131, B:A.206, C:M.152 Water bridges: B:D.132, B:F.133, B:G.209, B:G.209, B:G.209, C:V.154 TRS.13: 6 residues within 4Å: Chain B: M.152 Chain C: D.132, C.205, A.206, G.209, L.210 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.206, C:G.209, C:L.210, B:M.152 Water bridges: C:V.130, C:P.131, C:D.132, B:V.154 TRS.17: 4 residues within 4Å: Chain D: D.132, A.206, L.210 Chain E: M.152 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:D.132, D:A.206, E:M.152 Water bridges: D:D.132, D:F.133, D:F.133, D:S.208, E:T.110 TRS.18: 5 residues within 4Å: Chain D: M.37, D.38, N.39, P.40 Ligands: GOL.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.39, D:N.39 TRS.22: 7 residues within 4Å: Chain D: M.152 Chain E: D.132, C.205, A.206, G.209, L.210, K.211 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:D.132, E:D.132, E:C.205, E:G.209, E:L.210, D:M.152 Water bridges: E:P.131, E:D.132, E:K.211, E:A.212, D:T.110, D:T.110, D:V.154 TRS.24: 6 residues within 4Å: Chain F: Q.31, E.35, P.40, F.42, Y.52 Ligands: TRS.26 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.31 Water bridges: F:P.40 TRS.25: 5 residues within 4Å: Chain F: D.132, C.205, A.206, G.209, L.210 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:C.205, F:A.206, F:G.209, F:L.210 Water bridges: F:D.132 TRS.26: 2 residues within 4Å: Chain F: E.35 Ligands: TRS.24 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.35

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: S.208, G.209 Chain B: F.171 Chain F: Q.98, Q.187, D.188, G.190 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.98, F:Q.98 PEG.9: 6 residues within 4Å: Chain B: Q.187, D.188, G.190 Chain C: S.208, G.209 Chain D: F.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.187 PEG.14: 5 residues within 4Å: Chain B: S.208, G.209 Chain C: Q.98, Q.187, D.188 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:G.209 Hydrogen bonds: C:Q.98

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

CL.4: 5 residues within 4Å: Chain A: G.25, D.26, R.29, G.92 Chain B: R.47 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.167, Y.168 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: R.47 Chain B: 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, V.91 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: R.47 Chain D: G.25, D.26 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain E: R.47 Chain F: G.25, D.26, R.29, V.91 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: Q.82 Chain B: T.170, F.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.170 GOL.19: 5 residues within 4Å: Chain D: Q.31, E.35, P.40, F.42 Ligands: TRS.18 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.35, D:E.35, D:F.42 Water bridges: D:P.40, D:Y.52 GOL.27: 5 residues within 4Å: Chain B: T.172, G.173, R.174 Chain F: K.184, D.188 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:K.184, F:D.188, F:D.188 Water bridges: B:V.175

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

NA.11: 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:S.72, A:S.72, B:I.68, B:S.72 Water bridges: A:S.72 NA.29: 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:E.48, E:I.68, E:S.72 Water bridges: E:S.72

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

2016-07-20

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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