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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
Analyse Unique conformation of uridine and asymmetry of the hexameric molecule revealed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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