Research workbench
HPF1 bound to catalytic fragment of PARP2
Analyse HPF1 bound to catalytic fragment of PARP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TX3
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 2,POLY [ADP-ribose] polymerase 2; Histone parylation factor 1
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- Q9UGN5, Q9NWY4
- Ligands
- UHB
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Poly [ADP-ribose] polymerase 2,POLY [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 249 | 24% helix, 32% strand | Q9UGN5 |
| A | Histone parylation factor 1 | protein | 306 | 49% helix, 8% strand | Q9NWY4 |
Ligands and binding sites
- UHB · 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.70 | 0.77 | 53 | UHB |
| 2 | 72 | 0.42 | 0.80 | 23 | empty |
| 3 | 73 | 0.33 | 0.75 | 14 | empty |
| 4 | 71 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1384 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6TX3 · HPF1 bound to catalytic fragment of PARP2 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NWY4 · AlphaFold monomer V2.0 prediction for histone parylation factor 1 (Q9NWY4) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q9UGN5 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 2 (Q9UGN5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9UGN5
- Every structure of UniProt Q9NWY4
- Elsewhere: RCSB PDB 6TX3 · PDBe 6TX3 · UniProt Q9UGN5 · UniProt Q9NWY4
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