SMTL ID : 4ogk.1

X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

5 x THM: THYMIDINE(Non-covalent)

THM.1: 13 residues within 4Å: Chain A: I.69, G.70, R.91, G.93, T.94, F.162, Q.166, Y.195, E.196, M.197, E.198, I.220 Chain B: R.48 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.94, A:F.162, A:I.220 Hydrogen bonds: A:G.70, A:R.91, A:T.94, A:Q.166, A:Q.166, A:E.198 THM.4: 15 residues within 4Å: Chain A: F.7, H.8, R.48 Chain B: I.69, T.94, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.162, B:F.162, B:I.220, A:F.7 Hydrogen bonds: B:Q.166, B:Q.166, B:R.168, B:R.168, A:H.8 pi-Stacking: B:F.162 THM.6: 14 residues within 4Å: Chain C: F.7, H.8, R.48 Chain D: I.69, R.91, T.94, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:F.7 Hydrogen bonds: C:H.8, D:R.91, D:G.96, D:Q.166, D:Q.166, D:R.168 pi-Stacking: D:F.162 THM.8: 14 residues within 4Å: Chain E: I.69, R.91, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.162, E:I.220, E:V.221 Hydrogen bonds: E:R.91, E:T.94, E:G.96, E:Q.166, E:Q.166, E:R.168, E:R.168, E:E.198 THM.11: 14 residues within 4Å: Chain E: H.8, R.48 Chain F: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198, I.220, V.221 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.162, F:I.220 Hydrogen bonds: F:Q.166, F:Q.166, F:R.168, F:E.198, E:H.8, E:R.48 Water bridges: F:R.91 pi-Stacking: F:F.162

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 2 residues within 4Å: Chain A: R.251, L.253 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain A: P.28, S.46 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.46 EDO.5: 2 residues within 4Å: Chain C: H.101, V.153 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.153 Water bridges: C:H.101 EDO.10: 2 residues within 4Å: Chain E: A.231, E.232 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.232 EDO.13: 2 residues within 4Å: Chain F: H.101, V.153 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.153

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

PEG.7: 2 residues within 4Å: Chain D: N.230, M.234 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain D: H.101, T.111, V.153, G.154 Chain E: V.131, A.132, D.133 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:A.132, D:H.101, D:T.111

1 x K: POTASSIUM ION(Non-covalent)

K.12: 6 residues within 4Å: Chain E: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Metal complexes: F:E.49, F:I.69, E:E.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sotnichenko, S.E. et al., X-ray structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymidine at 2.40 A resolution. To be Published

Release Date

2015-03-04

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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