SMTL ID : 4of4.1

X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: E.49, I.69, S.73 Chain B: E.49, I.69, S.73 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:I.69, A:S.73, B:E.49, B:I.69, B:I.69, B:S.73 Water bridges: A:S.73 NA.6: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.49, D:I.69, D:S.73, C:E.49, C:I.69, C:S.73 Water bridges: C:S.73 NA.11: 6 residues within 4Å: Chain E: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:E.49, F:I.69, F:S.73, E:E.49, E:I.69, E:S.73 Water bridges: E:S.73

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

EDO.2: 4 residues within 4Å: Chain A: D.133, A.207, L.211 Chain D: I.155 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.133 Water bridges: A:F.134, D:T.111, D:I.155 EDO.4: 6 residues within 4Å: Chain B: P.25, G.26, R.91, I.92, G.93, T.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.26, B:T.94, B:T.94, B:T.94 Water bridges: B:D.27 EDO.5: 6 residues within 4Å: Chain A: G.118, L.121 Chain B: D.117, G.118, L.121, M.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.117 EDO.7: 4 residues within 4Å: Chain C: D.133, A.207, L.211 Chain F: I.155 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:D.133 Water bridges: C:F.134, F:T.111, F:I.155 EDO.9: 6 residues within 4Å: Chain D: P.25, G.26, R.91, I.92, G.93, T.94 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.26, D:T.94, D:T.94, D:T.94 Water bridges: D:D.27 EDO.10: 6 residues within 4Å: Chain C: G.118, L.121 Chain D: D.117, G.118, L.121, M.126 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.117 EDO.12: 4 residues within 4Å: Chain B: I.155 Chain E: D.133, A.207, L.211 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Water bridges: B:T.111, B:I.155, E:F.134 Hydrogen bonds: E:D.133 EDO.14: 6 residues within 4Å: Chain F: P.25, G.26, R.91, I.92, G.93, T.94 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.26, F:T.94, F:T.94, F:T.94 Water bridges: F:D.27 EDO.15: 6 residues within 4Å: Chain E: G.118, L.121 Chain F: D.117, G.118, L.121, M.126 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.117

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

PEG.3: 7 residues within 4Å: Chain A: S.208, Q.209, G.210 Chain B: F.172 Chain D: S.189, M.190, G.191 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:G.191, A:G.210 PEG.8: 7 residues within 4Å: Chain C: S.208, Q.209, G.210 Chain D: F.172 Chain F: S.189, M.190, G.191 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Water bridges: F:G.191, C:G.210 PEG.13: 7 residues within 4Å: Chain B: S.189, M.190, G.191 Chain E: S.208, Q.209, G.210 Chain F: F.172 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Water bridges: B:G.191, E:G.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balaev, V.V. et al., X-ray structure of unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 A resolution. To be Published

Release Date

2015-02-18

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uridine phosphorylase

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