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Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine and potassium ion at 2.194A resolution
Analyse Crystal structure of the uridine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OEC
- Type
- protein
- Length
- 1,486 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- ANU, K
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 28% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 33% helix, 31% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 34% helix, 29% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 35% helix, 28% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 28% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 32% helix, 29% strand | P0A1F6 |
Ligands and binding sites
- ANU · 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil · ligand · 2 copies · chains A, B, E, F
- K · Potassium ion · metal · 3 copies · chains A, B, C, D, E, F
- 1PE · Pentaethylene glycol · additive · 3 copies · chains B, C, E, A, D, F
- GOL · Glycerol · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.79 | 0.80 | 94 | empty |
| 2 | 523 | 0.71 | 0.80 | 48 | empty |
| 3 | 399 | 0.70 | 0.81 | 49 | empty |
| 4 | 396 | 0.69 | 0.81 | 45 | empty |
| 5 | 418 | 0.68 | 0.80 | 44 | empty |
Interfaces
12 interfaces between chains.
- E–F · 2136 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2074 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2014 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1060 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1058 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2OEC · Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A1F6
- Elsewhere: RCSB PDB 2OEC · PDBe 2OEC · UniProt P0A1F6
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