SMTL ID : 4ny1.1

X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.7 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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 B, 4 interactions with chain A Hydrogen bonds: B:E.49, B:I.69, B:S.73, A:E.49, A:I.69, A:S.73 Water bridges: A:S.73 NA.7: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:E.49, C:I.69, C:S.73, D:I.69, D:I.69, D:S.73 Water bridges: C:S.73 NA.13: 6 residues within 4Å: Chain E: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:E.49, E:I.69, E:S.73, F:I.69, F:S.73, F:S.73 Water bridges: E:S.73

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

EDO.2: 2 residues within 4Å: Chain A: R.87, T.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.87, A:T.88, A:T.88 Water bridges: A:T.20 EDO.3: 4 residues within 4Å: Chain A: D.133, A.207, L.211 Chain F: I.155 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.132, A:D.133, A:D.133, A:F.134 EDO.4: 3 residues within 4Å: Chain A: G.105, T.237, H.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.105 EDO.6: 6 residues within 4Å: Chain A: R.48 Chain B: R.30, R.91, G.93, T.94, E.198 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Water bridges: A:R.48, A:R.48 Hydrogen bonds: B:R.30, B:R.91, B:T.94, B:T.94, B:E.198 EDO.8: 2 residues within 4Å: Chain C: R.87, T.88 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.87, C:T.88, C:T.88 Water bridges: C:T.20 EDO.9: 4 residues within 4Å: Chain B: I.155 Chain C: D.133, A.207, L.211 4 PLIP interactions: 4 interactions with chain C Water bridges: C:A.132, C:D.133, C:D.133, C:F.134 EDO.10: 3 residues within 4Å: Chain C: G.105, T.237, H.240 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.105 EDO.12: 6 residues within 4Å: Chain C: R.48 Chain D: R.30, R.91, G.93, T.94, E.198 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.30, D:R.91, D:T.94, D:T.94, D:E.198 Water bridges: C:R.48, C:R.48 EDO.14: 2 residues within 4Å: Chain E: R.87, T.88 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.87, E:T.88, E:T.88 Water bridges: E:T.20 EDO.15: 4 residues within 4Å: Chain D: I.155 Chain E: D.133, A.207, L.211 4 PLIP interactions: 4 interactions with chain E Water bridges: E:A.132, E:D.133, E:D.133, E:F.134 EDO.16: 3 residues within 4Å: Chain E: G.105, T.237, H.240 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.105 EDO.18: 6 residues within 4Å: Chain E: R.48 Chain F: R.30, R.91, G.93, T.94, E.198 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.30, F:R.91, F:T.94, F:T.94, F:E.198 Water bridges: E:R.48, E:R.48

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

PEG.5: 7 residues within 4Å: Chain A: S.189, M.190, G.191 Chain E: F.172 Chain F: S.208, Q.209, G.210 1 PLIP interactions: 1 interactions with chain F Water bridges: F:G.210 PEG.11: 7 residues within 4Å: Chain A: F.172 Chain B: S.208, Q.209, G.210 Chain C: S.189, M.190, G.191 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.210 PEG.17: 7 residues within 4Å: Chain C: F.172 Chain D: S.208, Q.209, G.210 Chain E: S.189, M.190, G.191 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balaev, V.V. et al., X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis at 1.7 A resolution. TO BE PUBLISHED

Release Date

2015-01-07

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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