MolNFT v1 · #74561 · protein
Structure of HUPP2 in an inactive conformation with bound 5- benzylacyclouridine
3P0F · Uridine phosphorylase 2: “Structure of HUPP2 in an inactive conformation with bound 5- benzylacyclouridine”. X-ray diffraction, 3 ligands (BAU, CO, MG), 3 pockets (best druggability 0.59). MolNFT v1 #74561 on GenesisL1: 3D…
- PDB
- 3P0F
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase 2
- EC
- 2.4.2.3
- UniProt
- O95045
- Ligands
- BAU, CO, MG
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase 2 (EC 2.4.2.3) | protein | 293 | 35% helix, 26% strand | O95045 |
Ligands and binding sites
- BAU · 1-((2-hydroxyethoxy)methyl)-5-benzylpyrimidine-2,4(1H,3H)-dione · ligand · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.59 | 0.78 | 29 | empty |
| 2 | 186 | 0.54 | 0.79 | 26 | BAU |
| 3 | 138 | 0.48 | 0.78 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3P0F · Structure of hUPP2 in an inactive conformation with bound 5-benzylacyclouridine · the same entry in another collection · chain A against A, TM-score 1.00
- O95045 · AlphaFold monomer V2.0 prediction for uridine phosphorylase 2 (O95045) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O95045
- Elsewhere: RCSB PDB 3P0F · PDBe 3P0F · UniProt O95045
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.