SMTL ID : 2hrd.1

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: P.25, G.26, D.27, R.30, R.91, I.92, G.93, T.94, E.198 Chain F: R.48 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain A Salt bridges: F:R.48, A:R.30, A:R.91 Hydrogen bonds: A:G.26, A:D.27, A:T.94, A:T.94 Water bridges: A:R.91 PO4.2: 3 residues within 4Å: Chain A: R.178 Chain B: R.178 Chain C: R.178 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Salt bridges: A:R.178, C:R.178, B:R.178 PO4.5: 9 residues within 4Å: Chain B: P.25, G.26, R.30, R.91, I.92, G.93, T.94, E.198 Chain D: R.48 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.26, B:D.27, B:I.92, B:T.94, B:T.94 Water bridges: B:R.91, B:R.91 Salt bridges: B:R.30, B:R.91, D:R.48 PO4.9: 9 residues within 4Å: Chain C: P.25, G.26, D.27, R.91, I.92, G.93, T.94, E.198 Chain E: R.48 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.26, C:D.27, C:I.92, C:T.94, C:T.94 Salt bridges: C:R.91, E:R.48 PO4.12: 9 residues within 4Å: Chain B: R.48 Chain D: P.25, G.26, R.30, R.91, I.92, G.93, T.94, E.198 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.26, D:T.94, D:T.94 Water bridges: D:R.91 Salt bridges: D:R.30, D:R.91, B:R.48 PO4.14: 10 residues within 4Å: Chain C: R.48 Chain E: P.25, G.26, D.27, R.30, R.91, I.92, G.93, T.94, E.198 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.26, E:D.27, E:T.94, E:T.94, E:T.94 Water bridges: E:R.91 Salt bridges: E:R.30, E:R.91, C:R.48 PO4.17: 10 residues within 4Å: Chain A: R.48 Chain F: P.25, G.26, D.27, R.30, R.91, I.92, G.93, T.94, E.198 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain F Salt bridges: A:R.48, F:R.30, F:R.91 Hydrogen bonds: F:G.26, F:D.27, F:T.94, F:T.94 Water bridges: F:R.91 PO4.18: 3 residues within 4Å: Chain D: R.178 Chain E: R.178 Chain F: R.178 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Salt bridges: E:R.178, F:R.178, D:R.178

6 x TDR: THYMINE(Non-covalent)

TDR.3: 12 residues within 4Å: Chain A: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.162, A:I.220, A:V.221, A:P.229 Hydrogen bonds: A:T.94, A:G.96, A:Q.166, A:Q.166, A:R.168, A:R.168 Water bridges: A:T.94, A:M.197 TDR.6: 11 residues within 4Å: Chain B: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.162, B:I.220, B:V.221 Hydrogen bonds: B:T.94, B:Q.166, B:Q.166, B:R.168, B:R.168 Water bridges: B:T.94, B:M.197 TDR.10: 12 residues within 4Å: Chain C: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.162, C:I.220, C:V.221, C:P.229 Hydrogen bonds: C:T.94, C:T.94, C:Q.166, C:Q.166, C:R.168, C:R.168 Water bridges: C:M.197 TDR.13: 12 residues within 4Å: Chain D: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.162, D:I.220, D:V.221, D:P.229 Hydrogen bonds: D:T.94, D:G.96, D:Q.166, D:Q.166, D:R.168, D:R.168 Water bridges: D:T.94, D:M.197 TDR.15: 12 residues within 4Å: Chain E: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.162, E:I.220, E:V.221, E:P.229 Hydrogen bonds: E:T.94, E:T.94, E:Q.166, E:Q.166, E:R.168, E:R.168 Water bridges: E:M.197 TDR.19: 11 residues within 4Å: Chain F: T.94, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.162, F:I.220, F:V.221, F:P.229 Hydrogen bonds: F:T.94, F:T.94, F:Q.166, F:Q.166, F:R.168, F:R.168 Water bridges: F:M.197

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: T.111, V.131, A.132, D.133, F.134, T.137 Chain E: T.111, V.131, A.132, D.133, F.134, T.137 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:T.111, A:A.132, A:D.133, E:T.137, E:T.137 GOL.8: 3 residues within 4Å: Chain B: Y.172, S.173 Chain D: Q.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.172 GOL.11: 12 residues within 4Å: Chain C: T.111, V.131, A.132, D.133, F.134, T.137 Chain D: T.111, V.131, A.132, D.133, F.134, T.137 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.133, C:D.133, C:T.137 GOL.16: 4 residues within 4Å: Chain E: M.184, R.223, T.224, Q.225 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.224 GOL.20: 11 residues within 4Å: Chain B: T.111, V.131, A.132, D.133, F.134, T.137 Chain F: T.111, A.132, D.133, F.134, T.137 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:T.137, F:T.137, B:D.133

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 7 residues within 4Å: Chain B: E.167, G.182, M.184, E.185, R.223, T.224, Q.225 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.182, B:M.184, B:E.185 Water bridges: B:Y.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution. To be Published

Release Date

2007-07-24

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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