MolNFT v1 · #105369 · protein
Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine
4R2X: “Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution…”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.77). MolNFT v1 #105369 on GenesisL1: 3D structure…
- PDB
- 4R2X
- Type
- protein
- Length
- 1,460 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
- SO4, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 31% helix, 29% strand | Q8E9X9 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 32% helix, 29% 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, 30% strand | Q8E9X9 |
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 31% helix, 30% strand | Q8E9X9 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 34% helix, 29% strand | Q8E9X9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains C, D, E, A, F, B
- CL · Chloride ion · ion · 4 copies · chains C, D, F, A
- GOL · Glycerol · additive · 19 copies · chains C, D, F, E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.77 | 0.80 | 93 | GOL |
| 2 | 136 | 0.66 | 0.88 | 31 | SO4, CL, GOL |
| 3 | 193 | 0.63 | 0.84 | 41 | SO4, CL, GOL |
| 4 | 207 | 0.62 | 0.83 | 40 | SO4, CL, GOL |
| 5 | 262 | 0.61 | 0.80 | 49 | SO4, CL, GOL |
Interfaces
12 interfaces between chains.
- C–D · 2092 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2057 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2048 Ų buried · 20 hydrogen bonds · protein-protein
- E–B · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1099 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4R2X · Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the… · the same entry in another collection · chain C against C, 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 4R2X · PDBe 4R2X · UniProt Q8E9X9
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