MolNFT v1 · #102576 · protein + DNA
Structure of human parp-1 bound to a DNA double strand break in complex with (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7- carboxamide
4OPX · Poly [ADP-ribose] polymerase 1: “Structure of human parp-1 bound to a DNA double strand break in complex with…”. X-ray diffraction, 2 ligands (2UR, ZN), 18 pockets (best druggability 0.79). MolNFT v1 #102576 on GenesisL1: 3D…
- PDB
- 4OPX
- Type
- protein + DNA
- Length
- 1,408 residues
- Chains
- 6
- 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
- 2UR, ZN
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Poly [ADP-ribose] polymerase 1 | protein | 222 | 35% helix, 17% strand | P09874 |
| C, F | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 456 | 31% helix, 24% strand | P09874 |
| M, N | DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- 2UR · (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide · ligand · chains C
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.79 | 0.81 | 92 | empty |
| 2 | 821 | 0.78 | 0.82 | 72 | empty |
| 3 | 529 | 0.78 | 0.85 | 48 | empty |
| 4 | 566 | 0.78 | 0.84 | 49 | 2UR |
| 5 | 59 | 0.60 | 0.91 | 13 | empty |
Interfaces
9 interfaces between chains.
- M–N · 1139 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–C · 751 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 747 Ų buried · 11 hydrogen bonds · protein-protein
- A–N · 475 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–M · 460 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4OPX · Structure of Human PARP-1 bound to a DNA double strand break in complex with… · 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 4OPX · PDBe 4OPX · UniProt P09874
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