Research workbench
Crystal structure of C212S mutant of shewanella oneidensis mr-1 uridine phosphorylase
Analyse Crystal structure of C212S mutant of shewanella oneidensis mr-1 uridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YJK
- 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
- Q8E9X9
- Ligands
- URA, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 31% helix, 28% strand | Q8E9X9 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 30% strand | Q8E9X9 |
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 31% helix, 29% strand | Q8E9X9 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 33% helix, 29% strand | Q8E9X9 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 34% helix, 30% strand | Q8E9X9 |
Ligands and binding sites
- URA · Uracil · ligand · 3 copies · chains D, F, A
- SO4 · Sulfate ion · ion · 9 copies · chains D, C, F, B, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.77 | 0.84 | 53 | empty |
| 2 | 348 | 0.71 | 0.83 | 39 | empty |
| 3 | 264 | 0.66 | 0.83 | 36 | SO4 |
| 4 | 169 | 0.64 | 0.85 | 29 | URA, SO4 |
| 5 | 260 | 0.64 | 0.82 | 43 | URA, SO4 |
Interfaces
12 interfaces between chains.
- D–C · 2090 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2047 Ų buried · 22 hydrogen bonds · protein-protein
- F–E · 2044 Ų buried · 24 hydrogen bonds · protein-protein
- F–C · 1134 Ų buried · 9 hydrogen bonds · protein-protein
- E–B · 1125 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YJK · Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase · the same entry in another collection · chain D against D, 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 4YJK · PDBe 4YJK · UniProt Q8E9X9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.