Research workbench
Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
Analyse Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X0M
- Type
- protein + DNA
- Length
- 1,472 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone parylation factor 1; Poly [ADP-ribose] polymerase 2; DNA (167-mer)
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- Q9NWY4, Q9UGN5
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Histone parylation factor 1 | protein | 246 | 45% helix, 9% strand | Q9NWY4 |
| P | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 470 | 31% helix, 26% strand | Q9UGN5 |
| o | Histone parylation factor 1 | protein | 242 | 43% helix, 9% strand | Q9NWY4 |
| p | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 468 | 32% helix, 26% strand | Q9UGN5 |
| I | DNA (167-mer) | dna | 12 | — | — |
| J | DNA (167-mer) | dna | 12 | — | — |
| i | DNA (167-mer) | dna | 11 | — | — |
| j | DNA (167-mer) | dna | 11 | — | — |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.86 | 0.88 | 106 | empty |
| 2 | 1072 | 0.85 | 0.86 | 97 | empty |
| 3 | 1167 | 0.74 | 0.77 | 83 | empty |
| 4 | 635 | 0.70 | 0.78 | 72 | empty |
| 5 | 55 | 0.67 | 0.95 | 24 | empty |
Interfaces
18 interfaces between chains.
- O–P · 1303 Ų buried · 14 hydrogen bonds · protein-protein
- o–p · 1268 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 562 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- i–j · 511 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- p–i · 274 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6X0M · Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin · the same entry in another collection · chain j against j, TM-score 1.00
- Q9NWY4 · AlphaFold monomer V2.0 prediction for histone parylation factor 1 (Q9NWY4) · a predicted model of the same protein · chain o against A, TM-score 0.98
- Q9UGN5 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase 2 (Q9UGN5) · a predicted model of the same protein · chain p against A, TM-score 0.93
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 Q9NWY4
- Every structure of UniProt Q9UGN5
- Elsewhere: RCSB PDB 6X0M · PDBe 6X0M · UniProt Q9NWY4 · UniProt Q9UGN5
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