Research workbench
Structure of human PARP1 domains (ZN1, ZN3, wgr and hd) bound to a DNA double strand break.
Analyse Structure of human PARP1 domains (ZN1, ZN3, wgr and hd) bound to a DNA double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S68
- Type
- protein + DNA
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'); Poly [ADP-ribose] polymerase 1; Fusion of…
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N | DNA (5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3') | dna | 10 | — | — |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 211 | 41% helix, 18% strand | P09874 |
| A | Fusion of PARP1 zinc fingers 1 and 3 (ZN1, ZN3) (EC 2.4.2.30, 2.4.2.-) | protein | 223 | 33% helix, 16% strand | P09874 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.81 | 0.84 | 86 | empty |
| 2 | 328 | 0.56 | 0.75 | 44 | empty |
| 3 | 119 | 0.54 | 0.82 | 21 | empty |
| 4 | 116 | 0.53 | 0.82 | 24 | empty |
| 5 | 126 | 0.50 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–A · 788 Ų buried · 10 hydrogen bonds · protein-protein
- N–A · 477 Ų buried · 15 hydrogen bonds · protein-nucleic
- M–N · 459 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- M–A · 248 Ų buried · 4 hydrogen bonds · protein-nucleic
- M–B · 218 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 7S68 · Structure of human PARP1 domains (Zn1, Zn3, WGR and HD) bound to a DNA double strand… · the same entry in another collection · chain N against N, 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 7S68 · PDBe 7S68 · UniProt P09874
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