MolNFT v1 · #147946 · protein + DNA
Nucleosome breathing : class 2
6ESG · Histone H3.2: “Nucleosome breathing : class 2”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #147946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ESG
- Type
- protein + DNA
- Length
- 1,007 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 (141-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 8 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 64% helix, 4% strand | P84233 |
| B, F | Histone H4 | protein | 78 | 59% helix, 6% strand | P62799 |
| C | Histone H2A | protein | 100 | 55% helix, 5% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 89 | 76% helix, 3% strand | P02281 |
| E | Histone H3.2 | protein | 92 | 65% helix, 4% strand | P84233 |
| G | Histone H2A | protein | 102 | 53% helix, 5% strand | Q6AZJ8 |
| I | DNA (141-mer) | dna | 141 | — | — |
| J | DNA (141-mer) | dna | 141 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.80 | 0.82 | 112 | empty |
| 2 | 635 | 0.77 | 0.82 | 83 | empty |
| 3 | 480 | 0.74 | 0.83 | 42 | empty |
| 4 | 61 | 0.72 | 0.97 | 20 | empty |
| 5 | 60 | 0.72 | 0.97 | 20 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6695 Ų buried · 749 hydrogen bonds · nucleic-nucleic
- G–H · 2386 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2336 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2322 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2195 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6ESG · Nucleosome breathing : Class 2 · 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
- Elsewhere: RCSB PDB 6ESG · PDBe 6ESG · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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