Research workbench
Crystal structure of the catalytic domain of human PARP1 (apo)
Analyse Crystal structure of the catalytic domain of human PARP1 (apo) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AAA
- 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
- SO4
- Pockets
- 8 · best druggability 0.82
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
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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 | 1045 | 0.82 | 0.83 | 83 | SO4, EDO, DMS |
| 2 | 382 | 0.80 | 0.89 | 39 | DMS |
| 3 | 157 | 0.48 | 0.77 | 31 | empty |
| 4 | 100 | 0.45 | 0.79 | 18 | empty |
| 5 | 125 | 0.44 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7AAA · Crystal structure of the catalytic domain of human PARP1 (apo) · 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 7AAA · PDBe 7AAA · UniProt P09874
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