MolNFT v1 · #108126 · protein
Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor PJ34
4UXB · Poly ADP-ribose polymerase 1: “Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor PJ34”. X-ray diffraction, 2 ligands (P34, SO4), 9 pockets (best druggability 0.80). MolNFT v1 #108126 on GenesisL1: 3D structure…
- PDB
- 4UXB
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly ADP-ribose polymerase 1
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- P34, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly ADP-ribose polymerase 1 (EC 2.4.2.30) | protein | 323 | 37% helix, 24% strand | P09874 |
| B | Poly ADP-ribose polymerase 1 (EC 2.4.2.30) | protein | 336 | 38% helix, 23% strand | P09874 |
Ligands and binding sites
- P34 · N~2~,N~2~-dimethyl-N~1~-(6-oxo-5,6-dihydrophenanthridin-2-yl)glycinamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.80 | 0.86 | 39 | P34 |
| 2 | 482 | 0.78 | 0.86 | 39 | P34 |
| 3 | 129 | 0.53 | 0.82 | 15 | empty |
| 4 | 106 | 0.49 | 0.81 | 20 | empty |
| 5 | 122 | 0.45 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4UXB · Human ARTD1 (PARP1) - Catalytic domain in complex with inhibitor PJ34 · the same entry in another collection · chain B against B, TM-score 1.00
- P09874 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 1 (P09874) · a predicted model of the same protein · chain A 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 P09874
- Elsewhere: RCSB PDB 4UXB · PDBe 4UXB · UniProt P09874
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