MolNFT v1 · #89498 · protein + DNA
Structure of human parp-1 bound to a DNA double strand break
4DQY · Poly [ADP-ribose] polymerase 1: “Structure of human parp-1 bound to a DNA double strand break”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.79). MolNFT v1 #89498 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DQY
- Type
- protein + DNA
- Length
- 1,408 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1; DNA (26-mer)
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Poly [ADP-ribose] polymerase 1 | protein | 86 | 23% helix, 28% strand | P09874 |
| B, E | Poly [ADP-ribose] polymerase 1 | protein | 136 | 43% helix, 10% strand | P09874 |
| C, F | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 456 | 30% helix, 23% strand | P09874 |
| M, N | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.79 | 0.82 | 90 | empty |
| 2 | 627 | 0.78 | 0.84 | 72 | empty |
| 3 | 567 | 0.77 | 0.84 | 46 | EDO |
| 4 | 546 | 0.77 | 0.84 | 47 | empty |
| 5 | 236 | 0.62 | 0.82 | 45 | empty |
Interfaces
17 interfaces between chains.
- M–N · 1139 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- A–B · 539 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 506 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 469 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4DQY · Structure of Human PARP-1 bound to a DNA double strand break · 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 4DQY · PDBe 4DQY · UniProt P09874
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