Research workbench
Trapping of an oxocarbenium ion intermediate in up crystals
Analyse Trapping of an oxocarbenium ion intermediate in up crystals in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KVY
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- UniProt
- A5PJH9
- Ligands
- URA, R2B, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase | protein | 290 | 35% helix, 27% strand | A5PJH9 |
| B | Uridine phosphorylase | protein | 293 | 34% helix, 26% strand | A5PJH9 |
Ligands and binding sites
- URA · Uracil · ligand · 2 copies · chains A, B
- R2B · 1,4-anhydro-D-erythro-pent-1-enitol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.79 | 0.88 | 53 | empty |
| 2 | 149 | 0.78 | 0.95 | 34 | SO4, URA, R2B |
| 3 | 376 | 0.72 | 0.83 | 55 | SO4, URA, R2B |
| 4 | 212 | 0.62 | 0.82 | 35 | empty |
| 5 | 203 | 0.51 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2961 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3KVY · Trapping of an oxocarbenium ion intermediate in UP crystals · 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 A5PJH9
- Elsewhere: RCSB PDB 3KVY · PDBe 3KVY · UniProt A5PJH9
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