MolNFT v1 · #167431 · protein
Crystal structure of human parp-1 cat domain bound to inhibitor rucaparib
6VKK · Poly [ADP-ribose] polymerase 1: “Crystal structure of human parp-1 cat domain bound to inhibitor rucaparib”. X-ray diffraction, 2 ligands (RPB, SO4), 16 pockets (best druggability 0.81). MolNFT v1 #167431 on GenesisL1: 3D structure…
- PDB
- 6VKK
- Type
- protein
- Length
- 1,369 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, 2.4.2.-
- UniProt
- P09874
- Ligands
- RPB, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 26% 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 | 345 | 39% helix, 26% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 339 | 40% helix, 26% strand | P09874 |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 340 | 40% helix, 25% strand | P09874 |
Ligands and binding sites
- RPB · Rucaparib · ligand · 4 copies · chains A, D, C, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, C
- GOL · Glycerol · additive · 3 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.81 | 0.84 | 90 | SO4 |
| 2 | 574 | 0.79 | 0.85 | 50 | RPB, SO4 |
| 3 | 611 | 0.78 | 0.84 | 51 | RPB, SO4 |
| 4 | 1149 | 0.78 | 0.80 | 94 | SO4 |
| 5 | 545 | 0.78 | 0.85 | 45 | RPB, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 534 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 491 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 482 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 348 Ų buried · 0 hydrogen bonds · protein-protein
- D–B · 160 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VKK · Crystal Structure of human PARP-1 CAT domain bound to inhibitor rucaparib · the same entry in another collection · chain D against D, 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 6VKK · PDBe 6VKK · UniProt P09874
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