Research workbench
Crystal structure of human parp-1 cat domain bound to inhibitor eb-47
Analyse Crystal structure of human parp-1 cat domain bound to inhibitor eb-47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKQ
- Type
- protein
- Length
- 1,360 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
- UHB, SO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 340 | 34% helix, 23% strand | P09874 |
Ligands and binding sites
- UHB · 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.80 | 0.87 | 46 | UHB |
| 2 | 501 | 0.78 | 0.85 | 40 | UHB |
| 3 | 505 | 0.78 | 0.85 | 39 | UHB |
| 4 | 527 | 0.77 | 0.84 | 43 | UHB |
| 5 | 735 | 0.73 | 0.79 | 85 | empty |
Interfaces
3 interfaces between chains.
- A–B · 494 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 494 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 492 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VKQ · Crystal Structure of human PARP-1 CAT domain bound to inhibitor EB-47 · 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 6VKQ · PDBe 6VKQ · UniProt P09874
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