Research workbench
Crystal structure of the catalytic domain of human PARP1 in complex with inhibitor eb-47
Analyse Crystal structure of the catalytic domain of human PARP1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AAB
- Type
- protein
- Length
- 700 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, 2.4.2.-
- UniProt
- P09874
- Ligands
- UHB, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 350 | 38% helix, 21% strand | P09874 |
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 · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.75 | 0.80 | 61 | UHB |
| 2 | 648 | 0.74 | 0.80 | 47 | UHB |
| 3 | 444 | 0.65 | 0.78 | 53 | empty |
| 4 | 58 | 0.46 | 0.84 | 14 | empty |
| 5 | 101 | 0.44 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 475 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7AAB · Crystal structure of the catalytic domain of human PARP1 in complex with inhibitor EB-47 · 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 P09874
- Elsewhere: RCSB PDB 7AAB · PDBe 7AAB · UniProt P09874
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