Research workbench
Crystal structure of the catalytic domain of human PARP1 in complex with olaparib
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
- 7AAD
- 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
- 09L, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% 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 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- 09L · 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.83 | 0.85 | 77 | 09L, SO4 |
| 2 | 462 | 0.80 | 0.88 | 46 | 09L, SO4 |
| 3 | 103 | 0.44 | 0.78 | 17 | empty |
| 4 | 75 | 0.43 | 0.80 | 18 | empty |
| 5 | 70 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 812 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7AAD · Crystal structure of the catalytic domain of human PARP1 in complex with olaparib · 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 7AAD · PDBe 7AAD · UniProt P09874
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