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Crystal structure of catalytic domain of human POLY(ADP-ribose) polymerase complexed with a quinoxaline-type inhibitor
Analyse Crystal structure of catalytic domain of human POLY(ADP-ribose) polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WOK
- Type
- protein
- Length
- 1,400 residues
- Chains
- 4
- 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
- CNQ
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Poly [ADP-ribose] polymerase-1 (EC 2.4.2.30) | protein | 350 | 35% helix, 21% strand | P09874 |
Ligands and binding sites
- CNQ · 3-(4-chlorophenyl)quinoxaline-5-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.83 | 0.86 | 92 | empty |
| 2 | 578 | 0.81 | 0.87 | 39 | CNQ |
| 3 | 450 | 0.79 | 0.87 | 38 | CNQ |
| 4 | 454 | 0.79 | 0.87 | 42 | CNQ |
| 5 | 473 | 0.79 | 0.86 | 40 | CNQ |
Interfaces
4 interfaces between chains.
- B–D · 998 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 979 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 647 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 599 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1WOK · Crystal structure of catalytic domain of human poly(ADP-ribose) polymerase complexed with… · 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 1WOK · PDBe 1WOK · UniProt P09874
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