Research workbench
Class 1 : canonical nucleosome
Analyse Class 1 : canonical nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FQ5
- Type
- protein + DNA
- Length
- 1,068 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (147-mer)
- UniProt
- P62799, Q6AZJ8, A0A1L8FQ56
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 8 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 98 | 65% helix, 4% strand | — |
| B | Histone H4 | protein | 84 | 61% helix, 7% strand | P62799 |
| C, G | Histone H2A | protein | 110 | 54% helix, 6% strand | Q6AZJ8 |
| D, H | Histone H2B | protein | 95 | 72% helix, 4% strand | A0A1L8FQ56 |
| E | Histone H3 | protein | 97 | 66% helix, 4% strand | — |
| F | Histone H4 | protein | 85 | 59% helix, 8% strand | P62799 |
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
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 | 424 | 0.78 | 0.87 | 46 | empty |
| 2 | 438 | 0.77 | 0.86 | 55 | empty |
| 3 | 298 | 0.77 | 0.89 | 49 | empty |
| 4 | 338 | 0.72 | 0.85 | 39 | empty |
| 5 | 881 | 0.71 | 0.76 | 56 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6693 Ų buried · 621 hydrogen bonds · nucleic-nucleic
- G–H · 2622 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2583 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2575 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2570 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6FQ5 · Class 1 : canonical nucleosome · the same entry in another collection · chain I against I, 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 P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt A0A1L8FQ56
- Elsewhere: RCSB PDB 6FQ5 · PDBe 6FQ5 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQ56
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