Research workbench
Nucleosome breathing : class 3
Analyse Nucleosome breathing : class 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ESH
- Type
- protein + DNA
- Length
- 1,012 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 (137-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 64% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 81 | 62% helix, 7% strand | P62799 |
| C | Histone H2A | protein | 100 | 56% helix, 6% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 91 | 75% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 66% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 80 | 63% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 104 | 53% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 89 | 79% helix, 4% strand | P02281 |
| I | DNA (137-mer) | dna | 137 | — | — |
| J | DNA (137-mer) | dna | 137 | — | — |
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 | 869 | 0.82 | 0.84 | 118 | empty |
| 2 | 525 | 0.78 | 0.85 | 61 | empty |
| 3 | 72 | 0.74 | 0.97 | 21 | empty |
| 4 | 340 | 0.72 | 0.85 | 42 | empty |
| 5 | 552 | 0.69 | 0.79 | 49 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6331 Ų buried · 694 hydrogen bonds · nucleic-nucleic
- E–F · 2460 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2442 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2429 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2380 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ESH · Nucleosome breathing : Class 3 · the same entry in another collection · chain G against G, 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 6ESH · PDBe 6ESH · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.