SMTL ID : 5efo.1

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 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 B, 3 interactions with chain A Hydrogen bonds: B:E.48, B:I.68, B:S.72, A:E.48, A:I.68, A:S.72 Water bridges: B:S.72 NA.10: 6 residues within 4Å: Chain C: E.48, I.68, S.72 Chain D: E.48, I.68, S.72 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.68, C:S.72, C:S.72, D:I.68, D: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 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:E.48, F:I.68, F:S.72, F:S.72, E:E.48, E:I.68, E:S.72 Water bridges: F:S.72

6 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.2: 8 residues within 4Å: Chain A: G.95, F.161, Q.165, R.167, F.194, E.195, M.196 Ligands: TRS.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.165, A:Q.165, A:Q.165, A:R.167, A:R.167 Water bridges: A:G.95, A:G.95 CYT.5: 11 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 Ligands: GOL.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.95, B:Q.165, B:Q.165, B:Q.165, B:R.167, B:R.167 CYT.8: 8 residues within 4Å: Chain C: G.95, F.161, Q.165, R.167, F.194, E.195, M.196 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.165, C:Q.165, C:Q.165, C:R.167, C:R.167 CYT.9: 6 residues within 4Å: Chain A: R.177 Chain B: E.126 Chain C: R.178, F.179, S.182, W.186 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 interactions with chain C Water bridges: A:R.177 Hydrogen bonds: B:E.126, C:R.178, C:R.178, C:S.182, C:S.182 CYT.12: 10 residues within 4Å: Chain D: T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.220 Ligands: GOL.14 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.220 Hydrogen bonds: D:Q.165, D:Q.165, D:Q.165, D:R.167, D:R.167 CYT.13: 8 residues within 4Å: Chain D: L.115, R.178, F.179, S.182, E.185, W.186 Chain E: E.126 Chain F: R.177 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain D Hydrogen bonds: F:R.177, D:R.178, D:R.178 Hydrophobic interactions: D:L.115, D:R.178, D:F.179

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

TRS.3: 8 residues within 4Å: Chain A: I.68, F.161, E.195, M.196, E.197 Chain B: H.7, R.47 Ligands: CYT.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.196, A:E.197, B:H.7, B:R.47, B:R.47 Water bridges: A:R.90, A:R.90, A:R.90, A:R.90, A:E.195, A:E.197

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.7 Chain B: I.68, T.93, F.161, M.196, E.197 Ligands: CYT.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.7, A:R.47, B:T.93, B:E.197 Water bridges: A:R.47, A:R.47, A:R.47, B:T.93, B:T.93 GOL.6: 6 residues within 4Å: Chain C: I.68, E.195, M.196, E.197 Chain D: H.7 Ligands: CYT.8 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:M.196, D:H.7 Water bridges: C:R.90, C:T.93, C:F.194, C:E.197, D:R.47, D:R.47 GOL.14: 6 residues within 4Å: Chain C: H.7 Chain D: I.68, F.161, M.196, E.197 Ligands: CYT.12 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:E.197, C:H.7, C:R.47 Water bridges: D:R.90, D:T.93, D:T.93, D:T.93, D:E.197, C:R.47 GOL.16: 10 residues within 4Å: Chain E: P.24, G.25, D.26, R.29, R.90, V.91, G.92, T.93 Chain F: R.47 Ligands: CTN.17 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.25, E:D.26, E:R.29, E:R.29, E:R.29, F:R.47, F:R.47 Water bridges: E:R.90, E:R.90, E:T.93

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

PEG.7: 5 residues within 4Å: Chain C: Q.98, K.184, Q.187, D.188, G.190 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.184, C:D.188 Water bridges: C:Q.98, C:K.184

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

EDO.11: 3 residues within 4Å: Chain D: R.167, Y.168, D.169 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.168, D:D.169 Water bridges: D:R.167, D:R.167, D:D.169, D:R.222 EDO.18: 4 residues within 4Å: Chain E: F.6 Chain F: Y.162, R.167, D.169 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.169 Water bridges: F:R.167 EDO.19: 2 residues within 4Å: Chain E: L.120 Chain F: R.178 No protein-ligand interaction detected (PLIP)

2 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.17: 14 residues within 4Å: Chain E: 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 Ligands: GOL.16 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:I.219 Hydrogen bonds: E:T.93, E:Q.165, E:Q.165, E:R.167, E:R.167, E:M.196, F:H.7 Water bridges: E:R.90, E:R.90, E:T.93, E:E.197, E:E.197, F:R.47, F:R.47, F:R.47 CTN.20: 13 residues within 4Å: Chain E: H.7 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 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:T.93, F:Q.165, F:Q.165, F:R.167, F:R.167, F:M.196, E:H.7 Water bridges: F:R.90, F:T.93, E:R.47, E:R.47, E:R.47, E:R.47

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 uridine at 2.24 A resolution. To Be Published

Release Date

2016-11-09

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

Related Entries With Identical Sequence