SMTL ID : 4r2w.1

X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 in complex with uridine at 1.6 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.176 Chain C: R.176 Chain E: R.176 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C Salt bridges: A:R.176, E:R.176, C:R.176 SO4.2: 10 residues within 4Å: Chain A: P.23, G.24, R.28, R.89, V.90, G.91, T.92, E.196 Chain B: R.46 Ligands: GOL.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.24, A:D.25, A:T.92 Salt bridges: A:R.28, A:R.89, B:R.46 SO4.4: 8 residues within 4Å: Chain A: R.46 Chain B: G.24, R.28, R.89, V.90, G.91, T.92, E.196 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.24, B:D.25, B:T.92, B:T.92 Water bridges: B:R.89, B:E.194, A:R.46, A:R.46 Salt bridges: B:R.28, B:R.89, A:R.46 SO4.6: 9 residues within 4Å: Chain C: G.24, R.28, R.89, V.90, G.91, T.92, E.196 Chain D: R.46 Ligands: GOL.7 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Salt bridges: D:R.46, C:R.28, C:R.89 Hydrogen bonds: C:G.24, C:T.92, C:T.92 SO4.8: 11 residues within 4Å: Chain C: R.46 Chain D: P.23, G.24, D.25, R.28, R.89, V.90, G.91, T.92, E.196 Ligands: GOL.9 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.24, D:D.25, D:T.92, D:T.92 Salt bridges: D:R.28, D:R.89, C:R.46 SO4.11: 6 residues within 4Å: Chain E: G.24, R.89, V.90, T.92, E.196 Chain F: R.46 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.24, E:R.28, E:T.92, E:T.92 Salt bridges: E:R.89, F:R.46 Water bridges: F:R.46, F:R.46 SO4.13: 3 residues within 4Å: Chain B: R.176 Chain D: R.176 Chain F: R.176 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain D Salt bridges: F:R.176, B:R.176, D:R.176 SO4.14: 9 residues within 4Å: Chain E: R.46 Chain F: G.24, R.28, R.89, V.90, G.91, T.92, E.196 Ligands: URI.12 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.24, F:D.25, F:T.92 Salt bridges: F:R.28, F:R.89, E:R.46

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: I.67, R.89, T.92, T.93, E.194, M.195, E.196 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.89, A:T.92, A:T.92, A:M.195, A:E.196 GOL.5: 2 residues within 4Å: Chain B: N.131, A.205 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:A.205 Water bridges: B:N.131, B:F.132, B:G.208, E:G.189 GOL.7: 10 residues within 4Å: Chain C: I.67, R.89, T.92, T.93, Y.193, E.194, M.195, E.196 Chain D: R.46 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.89, C:T.92, C:M.195 Water bridges: C:Q.164 GOL.9: 9 residues within 4Å: Chain C: R.46 Chain D: I.67, R.89, T.92, T.93, E.194, M.195, E.196 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.89, D:T.92, D:T.92, D:M.195 Water bridges: D:T.92, D:T.92 GOL.10: 2 residues within 4Å: Chain D: N.131, A.205 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.205 Water bridges: A:Q.109, A:G.189 GOL.15: 2 residues within 4Å: Chain F: N.131, A.205 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.131, F:A.205 Water bridges: F:F.132, C:G.189

1 x URI: URIDINE(Non-covalent)

URI.12: 16 residues within 4Å: Chain E: F.5, H.6, R.46 Chain F: I.67, R.89, T.92, T.93, G.94, F.160, Q.164, R.166, Y.193, E.194, M.195, E.196 Ligands: SO4.14 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.160 Hydrogen bonds: F:R.89, F:T.92, F:T.92, F:G.94, F:Q.164, F:Q.164, F:R.166, F:R.166, F:M.195, F:E.196, E:H.6, E:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safonova, T.N. et al., High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-12-10

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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