Research workbench
Structure of the catalytic domain of PARP1 in complex with olaparib
Analyse Structure of the catalytic domain of PARP1 in complex with olaparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KK4
- Type
- protein
- Length
- 681 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
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 340 | 40% helix, 25% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 341 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.81 | 0.85 | 64 | 09L |
| 2 | 482 | 0.80 | 0.88 | 45 | 09L |
| 3 | 116 | 0.55 | 0.83 | 17 | empty |
| 4 | 130 | 0.49 | 0.79 | 16 | empty |
| 5 | 108 | 0.44 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KK4 · Structure of the catalytic domain of 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 7KK4 · PDBe 7KK4 · UniProt P09874
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