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
- 6X0L
- Type
- protein + DNA
- Length
- 934 residues
- Chains
- 7
- 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
- 13 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Histone parylation factor 1 | protein | 306 | 48% helix, 7% strand | Q9NWY4 |
| P | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 474 | 30% helix, 26% strand | Q9UGN5 |
| R | Poly [ADP-ribose] polymerase 2 (EC 2.4.2.30, 2.4.2.-) | protein | 114 | 14% helix, 38% strand | Q9UGN5 |
| I | DNA (167-mer) | dna | 10 | — | — |
| J | DNA (167-mer) | dna | 10 | — | — |
| i | DNA (167-mer) | dna | 10 | — | — |
| j | DNA (167-mer) | dna | 10 | — | — |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.87 | 0.88 | 107 | empty |
| 2 | 931 | 0.72 | 0.76 | 74 | empty |
| 3 | 88 | 0.69 | 0.94 | 17 | empty |
| 4 | 62 | 0.69 | 0.96 | 20 | empty |
| 5 | 410 | 0.66 | 0.79 | 51 | empty |
Interfaces
16 interfaces between chains.
- O–P · 1391 Ų buried · 8 hydrogen bonds · protein-protein
- i–j · 469 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- I–J · 459 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- P–J · 265 Ų buried · 8 hydrogen bonds · protein-nucleic
- P–I · 247 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6X0L · 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 0.99
- 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 6X0L · PDBe 6X0L · UniProt Q9NWY4 · UniProt Q9UGN5
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