Research workbench
Nucleosome : class 1
Analyse Nucleosome : class 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ESF
- Type
- protein + DNA
- Length
- 1,056 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (147-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 65% helix, 3% strand | P84233 |
| B | Histone H4 | protein | 84 | 58% helix, 7% strand | P62799 |
| C | Histone H2A | protein | 104 | 48% helix, 5% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 94 | 70% helix, 3% strand | P02281 |
| F | Histone H4 | protein | 85 | 58% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 105 | 50% helix, 7% strand | Q6AZJ8 |
| 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 | 849 | 0.81 | 0.83 | 87 | empty |
| 2 | 472 | 0.74 | 0.83 | 48 | empty |
| 3 | 381 | 0.74 | 0.85 | 42 | empty |
| 4 | 784 | 0.70 | 0.77 | 52 | empty |
| 5 | 525 | 0.67 | 0.78 | 45 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6653 Ų buried · 582 hydrogen bonds · nucleic-nucleic
- A–B · 2651 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2606 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2593 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2573 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6ESF · Nucleosome : Class 1 · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 6ESF · PDBe 6ESF · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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