MolNFT v1 · #187244 · protein + DNA
Human PARP1 DELTAV687-E688 bound to NAD+ analog eb-47 and to a DNA double strand break.
7S6H · DNA (5'-D(*CP*GP*AP*CP*G)-3'): “Human PARP1 DELTAV687-E688 bound to NAD+ analog eb-47 and to a DNA double strand break.”. X-ray diffraction, 2 ligands (UHB, ZN), 12 pockets (best druggability 0.85). MolNFT v1 #187244 on GenesisL1…
- PDB
- 7S6H
- Type
- protein + DNA
- Length
- 1,404 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*AP*CP*G)-3'); DNA (5'-D(*CP*GP*TP*CP*G)-3'); Poly [ADP-ribose]…
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P09874
- Ligands
- UHB, ZN
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, E | DNA (5'-D(*CP*GP*AP*CP*G)-3') | dna | 5 | — | — |
| N, F | DNA (5'-D(*CP*GP*TP*CP*G)-3') | dna | 5 | — | — |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 469 | 32% helix, 27% strand | P09874 |
| A | Fusion of human PARP1 zinc fingers 1 and 3 (ZN1, ZN3) (EC 2.4.2.30, 2.4.2.-) | protein | 223 | 37% helix, 16% strand | P09874 |
| C | Fusion of human PARP1 zinc fingers 1 and 3 (ZN1, ZN3) (EC 2.4.2.30, 2.4.2.-) | protein | 221 | 37% helix, 16% strand | P09874 |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 471 | 32% helix, 27% 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 · 2 copies · chains B, D
- ZN · Zinc ion · metal · 4 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.85 | 0.86 | 145 | empty |
| 2 | 831 | 0.79 | 0.82 | 56 | UHB |
| 3 | 811 | 0.78 | 0.82 | 56 | UHB |
| 4 | 520 | 0.66 | 0.77 | 61 | empty |
| 5 | 496 | 0.65 | 0.77 | 60 | empty |
Interfaces
16 interfaces between chains.
- B–A · 775 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 769 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 491 Ų buried · 15 hydrogen bonds · protein-protein
- N–A · 483 Ų buried · 10 hydrogen bonds · protein-nucleic
- F–C · 477 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 7S6H · Human PARP1 deltaV687-E688 bound to NAD+ analog EB-47 and 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 7S6H · PDBe 7S6H · UniProt P09874
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