MolNFT v1 · #105368 · protein
X-ray structure of uridine phosphorylase from shewanella oneidensis mr-1 in complex with uridine at 1.6 a resolution
4R2W: “X-ray structure of uridine phosphorylase from shewanella oneidensis mr-1 in complex with uridine at 1.6 a…”. X-ray diffraction, 2 ligands (URI, SO4), 17 pockets (best druggability 0.78). MolNFT v1 #105368 on GenesisL1: 3D structure…
- PDB
- 4R2W
- Type
- protein
- Length
- 1,464 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q8E9X9
- Ligands
- URI, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 33% helix, 30% strand | Q8E9X9 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 34% helix, 29% strand | Q8E9X9 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 32% helix, 29% strand | Q8E9X9 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 31% helix, 28% strand | Q8E9X9 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 34% helix, 29% strand | Q8E9X9 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 33% helix, 28% strand | Q8E9X9 |
Ligands and binding sites
- URI · Uridine · ligand · chains E, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, E, B, D, F
- GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.78 | 0.80 | 119 | SO4 |
| 2 | 262 | 0.68 | 0.84 | 44 | SO4, GOL |
| 3 | 117 | 0.65 | 0.89 | 26 | URI, SO4 |
| 4 | 145 | 0.65 | 0.87 | 26 | SO4, GOL |
| 5 | 234 | 0.64 | 0.83 | 33 | SO4 |
Interfaces
12 interfaces between chains.
- C–D · 2121 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2095 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2029 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1123 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1106 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4R2W · X-ray structure of uridine phosphorylase from Shewanella oneidensis MR-1 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 Q8E9X9
- Elsewhere: RCSB PDB 4R2W · PDBe 4R2W · UniProt Q8E9X9
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