SMTL ID : 6eyp.1

X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-hexamer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: I.68, E.195, M.196, E.197 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Water bridges: B:R.47, B:R.47, B:R.47, A:T.93, A:E.197 Hydrogen bonds: A:E.195, A:M.196, A:E.197 GOL.3: 5 residues within 4Å: Chain A: H.7, R.47 Chain B: F.161, M.196, E.197 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.7, A:R.47, B:M.196, B:E.197 Water bridges: A:R.47, B:R.90, B:T.93, B:T.93 GOL.4: 6 residues within 4Å: Chain C: I.68, F.161, M.196, E.197 Chain D: H.7, R.47 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.7, C:E.197 Water bridges: D:R.47, D:R.47, D:R.47, D:R.47, C:T.93 GOL.7: 6 residues within 4Å: Chain C: H.7, R.47 Chain D: I.68, F.161, M.196, E.197 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.197, C:H.7, C:R.47 Water bridges: D:T.93, C:R.47, C:R.47 GOL.8: 8 residues within 4Å: Chain D: R.178, F.179, S.182, E.185, W.186 Chain E: P.124, E.126 Chain F: R.177 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.126, F:R.177 GOL.9: 6 residues within 4Å: Chain E: I.68, F.161, M.196, E.197 Chain F: H.7, R.47 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:E.197, F:H.7 Water bridges: E:R.90, E:R.90, E:T.93, E:T.93, E:E.197, F:R.47, F:R.47 GOL.11: 4 residues within 4Å: Chain E: H.7, R.47 Chain F: F.161, E.197 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:H.7, E:R.47, F:E.197 Water bridges: E:R.47, F:T.93, F:T.93, F:T.93 GOL.12: 4 residues within 4Å: Chain A: E.126 Chain B: R.177 Chain F: R.178, E.185 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:R.178, F:R.178, F:E.185 Water bridges: B:R.177, B:R.177

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain C: N.102 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prokofev, I.I. et al., X-ray structure of the unliganded uridine phosphorylase from Vibrio cholerae at 1.22A. To Be Published

Release Date

2018-11-21

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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