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Structure of human PARP1 domains (ZN1, ZN3, wgr, hd) bound to a DNA double strand break.
Analyse Structure of human PARP1 domains (ZN1, ZN3, wgr, 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
- 7S81
- Type
- protein + DNA
- Length
- 1,754 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3'); Poly [ADP-ribose] polymerase 1
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P09874
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 13 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, L, E, D | DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3') | dna | 12 | — | — |
| C | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 213 | 39% helix, 22% strand | P09874 |
| K | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 203 | 37% helix, 23% strand | P09874 |
| N | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 89 | 22% helix, 27% strand | P09874 |
| I | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 87 | 23% helix, 28% strand | P09874 |
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 91 | 22% helix, 26% strand | P09874 |
| G | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 135 | 47% helix, 10% strand | P09874 |
| P | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 196 | 36% helix, 24% strand | P09874 |
| H | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 200 | 36% helix, 24% strand | P09874 |
| O | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 138 | 46% helix, 10% strand | P09874 |
| J | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 139 | 47% helix, 10% strand | P09874 |
| F | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 85 | 24% helix, 28% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 130 | 46% helix, 11% strand | P09874 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains N, I, A, G, O, J, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.81 | 0.84 | 91 | empty |
| 2 | 938 | 0.80 | 0.82 | 105 | empty |
| 3 | 759 | 0.80 | 0.84 | 87 | empty |
| 4 | 522 | 0.79 | 0.85 | 60 | empty |
| 5 | 795 | 0.68 | 0.75 | 83 | empty |
Interfaces
37 interfaces between chains.
- I–J · 600 Ų buried · 9 hydrogen bonds · protein-protein
- M–L · 565 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- E–D · 564 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–B · 564 Ų buried · 11 hydrogen bonds · protein-protein
- G–F · 545 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7S81 · Structure of human PARP1 domains (Zn1, Zn3, WGR, HD) bound to a DNA double strand break. · the same entry in another collection · chain M against M, 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 7S81 · PDBe 7S81 · UniProt P09874
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