MolNFT v1 · #59739 · protein
X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine at 2.38A resolution
3C74: “X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine…”. X-ray diffraction, 1 ligand (ANU), 16 pockets (best druggability 0.70). MolNFT v1 #59739 on GenesisL1: 3D structure…
- PDB
- 3C74
- Type
- protein
- Length
- 1,469 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
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 32% helix, 29% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 29% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 31% helix, 30% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 28% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 32% helix, 30% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 32% helix, 29% strand | P0A1F6 |
Ligands and binding sites
- ANU · 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil · ligand · 6 copies · chains A, F, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.70 | 0.81 | 53 | ANU |
| 2 | 388 | 0.68 | 0.81 | 46 | empty |
| 3 | 372 | 0.68 | 0.80 | 44 | empty |
| 4 | 338 | 0.67 | 0.82 | 47 | ANU |
| 5 | 213 | 0.66 | 0.84 | 30 | ANU |
Interfaces
12 interfaces between chains.
- B–D · 2165 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 2133 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 2109 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1046 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 1034 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3C74 · X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with… · 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 3C74 · PDBe 3C74 · UniProt P0A1F6
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