SMTL ID : 5miw.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-hexamer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.47 Chain B: G.25, D.26 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: G.25, D.26 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: T.110 Chain C: D.132, F.133 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: D.132, F.133 Chain E: T.110 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: P.24, G.25, D.26 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain E: G.25, D.26, R.29, G.92 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain F: P.24, G.25, D.26 Ligand excluded by PLIP

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

NA.2: 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 B, 3 interactions with chain A Hydrogen bonds: B:E.48, B:I.68, B:I.68, B:S.72, A:I.68, A:S.72 Water bridges: A:S.72 NA.3: 4 residues within 4Å: Chain A: F.133, T.137 Chain F: F.133, T.137 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.137 Water bridges: F:T.137 NA.13: 4 residues within 4Å: Chain B: F.133, T.137 Chain C: F.133, T.137 No protein-ligand interaction detected (PLIP) NA.20: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.68, C:I.68, C:S.72, D:I.68, D:S.72 Water bridges: C:S.72 NA.23: 4 residues within 4Å: Chain D: F.133, T.137 Chain E: F.133, T.137 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.137 Water bridges: D:T.137 NA.28: 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

6 x URA: URACIL(Non-covalent)

URA.4: 11 residues within 4Å: Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.220 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:G.95, A:Q.165, A:Q.165, A:R.167, A:R.167 URA.9: 12 residues within 4Å: Chain B: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.219, B:I.220 Hydrogen bonds: B:T.93, B:G.95, B:Q.165, B:Q.165, B:R.167, B:R.167 Water bridges: B:M.196 URA.17: 12 residues within 4Å: Chain C: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.18 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.93, C:T.93, C:G.95, C:Q.165, C:Q.165, C:R.167, C:R.167 URA.24: 8 residues within 4Å: Chain D: G.95, F.161, Q.165, R.167, F.194, E.195, M.196 Ligands: GOL.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.165, D:Q.165, D:R.167 URA.29: 12 residues within 4Å: Chain E: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220 Ligands: GOL.30 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:I.219 Hydrogen bonds: E:T.93, E:G.95, E:Q.165, E:Q.165, E:R.167, E:R.167 URA.32: 8 residues within 4Å: Chain F: G.95, F.161, Q.165, R.167, F.194, E.195, M.196 Ligands: GOL.33 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.165, F:Q.165, F:R.167, F:R.167

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

SO4.5: 3 residues within 4Å: Chain A: R.177 Chain C: R.177 Chain E: R.177 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:Q.180, A:R.177 SO4.10: 3 residues within 4Å: Chain B: R.177 Chain D: R.177 Chain F: R.177 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D, 2 interactions with chain F Water bridges: B:R.177, B:R.177, D:R.177, F:R.177 Salt bridges: B:R.177, D:R.177, F:R.177

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.90, T.93, F.161, E.197 Chain B: H.7, R.47 Ligands: URA.4 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.7, A:R.90, A:T.93, A:T.93, A:E.197 Water bridges: B:R.47, B:R.47, B:R.47, B:R.47, B:R.47 GOL.11: 5 residues within 4Å: Chain B: R.178, E.185 Chain C: P.124, E.126 Chain D: R.177 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.178, B:R.178, B:E.185, D:R.177 GOL.12: 8 residues within 4Å: Chain A: H.7 Chain B: I.68, R.90, T.93, F.161, M.196, E.197 Ligands: URA.9 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.7, A:R.47, B:R.90, B:T.93, B:E.197 Water bridges: A:R.47, A:R.47, A:R.47, A:R.47, B:T.93, B:T.93 GOL.18: 8 residues within 4Å: Chain C: I.68, T.93, F.161, M.196, E.197 Chain D: H.7, R.47 Ligands: URA.17 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:H.7, D:R.47, C:T.93, C:T.93, C:E.197 Water bridges: D:R.47, C:T.93, C:T.93 GOL.19: 5 residues within 4Å: Chain A: R.177 Chain B: P.124, E.126 Chain C: R.178, E.185 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.178, C:R.178, C:E.185, B:E.126 GOL.25: 5 residues within 4Å: Chain D: R.178, E.185 Chain E: P.124, E.126 Chain F: R.177 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: D:R.178, D:E.185, E:E.126, F:R.177 Water bridges: D:E.185 GOL.26: 6 residues within 4Å: Chain C: H.7 Chain D: I.68, F.161, M.196, E.197 Ligands: URA.24 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.7, D:E.197 Water bridges: C:R.47, C:R.47, D:R.90, D:R.90 GOL.30: 8 residues within 4Å: Chain E: I.68, R.90, T.93, F.161, M.196, E.197 Chain F: H.7 Ligands: URA.29 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:H.7, F:R.47, E:R.90, E:T.93, E:E.197 Water bridges: F:R.47, F:R.47, F:R.47, F:R.47, E:T.93, E:T.93 GOL.33: 6 residues within 4Å: Chain E: H.7 Chain F: I.68, F.161, M.196, E.197 Ligands: URA.32 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:E.197, E:H.7, E:R.47 Water bridges: F:R.90, F:R.90, F:T.93, F:E.197, E:R.47, E:R.47 GOL.34: 5 residues within 4Å: Chain A: P.124, E.126 Chain B: R.177 Chain F: R.178, E.185 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:R.177, F:R.178, F:R.178, F:E.185 Water bridges: B:R.177, F:E.185

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

EDO.8: 5 residues within 4Å: Chain A: D.169, T.170, F.171 Chain B: K.3, Q.82 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.3, B:Q.82, A:D.169 EDO.16: 4 residues within 4Å: Chain C: Q.82 Chain D: D.169, T.170, F.171 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.169, C:Q.82

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 uracil at 1.28 A. To Be Published

Release Date

2017-12-20

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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