MolNFT v1 · #69617 · protein
Trapping of an oxocarbenium ion intermediate in up crystals
3KVR · Uridine phosphorylase: “Trapping of an oxocarbenium ion intermediate in up crystals”. X-ray diffraction, 3 ligands (URF, R2G, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #69617 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KVR
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- A5PJH9
- Ligands
- URF, R2G, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 293 | 33% helix, 26% strand | A5PJH9 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 293 | 36% helix, 26% strand | A5PJH9 |
Ligands and binding sites
- URF · 5-fluorouracil · ligand · 2 copies · chains A, B
- R2G · 2,5-anhydro-4-deoxy-D-erythro-pent-4-enitol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.80 | 0.89 | 46 | empty |
| 2 | 83 | 0.74 | 0.97 | 26 | URF, SO4, R2G |
| 3 | 80 | 0.74 | 0.97 | 24 | URF, SO4, R2G |
| 4 | 186 | 0.60 | 0.82 | 33 | empty |
| 5 | 229 | 0.54 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2990 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3KVR · 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 3KVR · PDBe 3KVR · UniProt A5PJH9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.