Research workbench
Structure of HUPP2 in an active conformation with bound 5- benzylacyclouridine
Analyse Structure of HUPP2 in an active conformation with bound 5- benzylacyclouridine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P0E
- Type
- protein
- Length
- 1,722 residues
- Chains
- 6
- 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, PO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Uridine phosphorylase 2 (EC 2.4.2.3) | protein | 285 | 35% helix, 25% strand | O95045 |
| C, E | Uridine phosphorylase 2 (EC 2.4.2.3) | protein | 291 | 36% helix, 26% strand | O95045 |
Ligands and binding sites
- BAU · 1-((2-hydroxyethoxy)methyl)-5-benzylpyrimidine-2,4(1H,3H)-dione · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.77 | 0.85 | 59 | BAU, PO4 |
| 2 | 297 | 0.77 | 0.88 | 44 | empty |
| 3 | 435 | 0.76 | 0.85 | 57 | BAU, PO4 |
| 4 | 394 | 0.76 | 0.86 | 46 | empty |
| 5 | 391 | 0.76 | 0.86 | 61 | BAU, PO4 |
Interfaces
6 interfaces between chains.
- C–D · 3077 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3064 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3020 Ų buried · 42 hydrogen bonds · protein-protein
- B–F · 358 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 192 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3P0E · Structure of hUPP2 in an active conformation with bound 5-benzylacyclouridine · the same entry in another collection · chain F against F, 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 0.99
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 3P0E · PDBe 3P0E · UniProt O95045
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.