MolNFT v1 · #102191 · protein
X-ray structure of uridine phosphorylase from vibrio cholerae complexed with uracil at 1.91 a resolution
4OEH: “X-ray structure of uridine phosphorylase from vibrio cholerae complexed with uracil at 1.91 a resolution”. X-ray diffraction, 2 ligands (URA, NA), 16 pockets (best druggability 0.74). MolNFT v1 #102191 on GenesisL1: 3D structure…
- PDB
- 4OEH
- Type
- protein
- Length
- 1,506 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q9KT71
- Ligands
- URA, NA
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | Q9KT71 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 32% helix, 29% strand | Q9KT71 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 29% strand | Q9KT71 |
Ligands and binding sites
- URA · Uracil · ligand · 4 copies · chains A, B, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, E, F
- EOH · Ethanol · additive · 3 copies · chains A, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.74 | 0.82 | 77 | empty |
| 2 | 426 | 0.73 | 0.83 | 48 | GOL |
| 3 | 207 | 0.72 | 0.88 | 41 | URA, GOL |
| 4 | 368 | 0.72 | 0.84 | 45 | EDO, URA, GOL, EOH |
| 5 | 352 | 0.72 | 0.84 | 46 | GOL |
Interfaces
12 interfaces between chains.
- A–B · 2105 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2099 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1944 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1097 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1092 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4OEH · X-ray Structure of Uridine Phosphorylase from Vibrio cholerae Complexed with Uracil at… · 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 Q9KT71
- Elsewhere: RCSB PDB 4OEH · PDBe 4OEH · UniProt Q9KT71
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