Research workbench
Human PARP1 DELTAV687-E688 bound to a DNA double strand break.
Analyse Human PARP1 DELTAV687-E688 bound to a DNA double strand break. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S6M
- Type
- protein + DNA
- Length
- 1,399 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
- ZN
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, N | DNA (5'-D(*CP*GP*AP*CP*G)-3') | dna | 5 | — | — |
| P, M | DNA (5'-D(*CP*GP*TP*CP*G)-3') | dna | 5 | — | — |
| D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 471 | 32% helix, 27% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 467 | 33% 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 | 219 | 38% helix, 17% strand | P09874 |
| C | Fusion of human PARP1 zinc fingers 1 and 3 (ZN1, ZN3) (EC 2.4.2.30, 2.4.2.-) | protein | 222 | 39% helix, 17% strand | P09874 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains D, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.85 | 0.86 | 145 | empty |
| 2 | 867 | 0.79 | 0.81 | 69 | EDO |
| 3 | 656 | 0.77 | 0.82 | 53 | EDO |
| 4 | 557 | 0.68 | 0.78 | 63 | empty |
| 5 | 325 | 0.62 | 0.78 | 39 | empty |
Interfaces
16 interfaces between chains.
- D–C · 784 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 781 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 496 Ų buried · 14 hydrogen bonds · protein-protein
- P–C · 495 Ų buried · 11 hydrogen bonds · protein-nucleic
- M–A · 495 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 7S6M · Human PARP1 deltaV687-E688 bound to a DNA double strand break. · the same entry in another collection · chain O against O, 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 7S6M · PDBe 7S6M · UniProt P09874
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