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
- 6X0N
- Type
- protein + DNA
- Length
- 3,041 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (167-mer); Histone parylation…
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P84233, P62799, Q6AZJ8, P02281, Q9NWY4, Q9UGN5
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 17 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 65% helix, 4% strand | P84233 |
| B, F | Histone H4 | protein | 81 | 60% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 110 | 53% helix, 6% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 98 | 71% helix, 4% strand | P02281 |
| I | DNA (167-mer) | dna | 157 | — | — |
| J | DNA (167-mer) | dna | 157 | — | — |
| a | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| b, f | Histone H4 | protein | 78 | 63% helix, 9% strand | P62799 |
| c | Histone H2A | protein | 102 | 57% helix, 6% strand | Q6AZJ8 |
| d, h | Histone H2B 1.1 | protein | 92 | 74% helix, 4% strand | P02281 |
| e | Histone H3.2 | protein | 95 | 67% helix, 4% strand | P84233 |
| g | Histone H2A | protein | 106 | 57% helix, 7% strand | Q6AZJ8 |
| i | DNA (167-mer) | dna | 160 | — | — |
| j | DNA (167-mer) | dna | 160 | — | — |
| 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 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.84 | 0.88 | 73 | empty |
| 2 | 1105 | 0.77 | 0.79 | 77 | empty |
| 3 | 795 | 0.76 | 0.80 | 75 | empty |
| 4 | 777 | 0.71 | 0.77 | 52 | empty |
| 5 | 508 | 0.71 | 0.80 | 44 | empty |
Interfaces
88 interfaces between chains.
- I–J · 7312 Ų buried · 983 hydrogen bonds · nucleic-nucleic
- i–j · 7308 Ų buried · 786 hydrogen bonds · nucleic-nucleic
- E–F · 2584 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2570 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2566 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6X0N · Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin · the same entry in another collection · chain a against a, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt Q9NWY4
- Every structure of UniProt Q9UGN5
- Elsewhere: RCSB PDB 6X0N · PDBe 6X0N · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q9NWY4 · UniProt Q9UGN5
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