Research workbench
Human ARTD1 (PARP1) catalytic domain in complex with inhibitor rucaparib
Analyse Human ARTD1 (PARP1) catalytic domain in complex with inhibitor rucaparib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RV6
- Type
- protein
- Length
- 1,392 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
- RPB, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 347 | 38% helix, 24% strand | P09874 |
| B, D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 349 | 38% helix, 24% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 347 | 38% helix, 24% strand | P09874 |
Ligands and binding sites
- RPB · Rucaparib · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.78 | 0.87 | 38 | empty |
| 2 | 386 | 0.78 | 0.88 | 38 | RPB |
| 3 | 385 | 0.78 | 0.87 | 35 | empty |
| 4 | 385 | 0.77 | 0.87 | 40 | RPB |
| 5 | 511 | 0.75 | 0.83 | 49 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 658 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 645 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 596 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RV6 · Human ARTD1 (PARP1) catalytic domain in complex with inhibitor Rucaparib · 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 4RV6 · PDBe 4RV6 · UniProt P09874
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