Research workbench
H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract (oligo fraction)
Analyse H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBF
- Type
- protein + DNA
- Length
- 1,186 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (184-mer); Protein B4
- UniProt
- P84233, P62799, Q6DKE3, P02281, P15308
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 9 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 99 | 65% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 84 | 57% helix, 8% strand | P62799 |
| C, G | Histone H2A | protein | 105 | 53% helix, 5% strand | Q6DKE3 |
| D, H | Histone H2B 1.1 | protein | 95 | 71% helix, 2% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 64% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 84 | 58% helix, 8% strand | P62799 |
| I | DNA (184-mer) | dna | 172 | — | — |
| J | DNA (184-mer) | dna | 172 | — | — |
| K | Protein B4 | protein | 78 | 44% helix, 19% strand | P15308 |
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 | 1061 | 0.79 | 0.81 | 112 | empty |
| 2 | 1178 | 0.76 | 0.79 | 93 | empty |
| 3 | 95 | 0.76 | 0.97 | 29 | empty |
| 4 | 586 | 0.75 | 0.82 | 54 | empty |
| 5 | 97 | 0.73 | 0.94 | 27 | empty |
Interfaces
37 interfaces between chains.
- I–J · 7682 Ų buried · 835 hydrogen bonds · nucleic-nucleic
- E–F · 2522 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2383 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2378 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2349 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7KBF · H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo… · the same entry in another collection · chain I against I, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q6DKE3
- Every structure of UniProt P02281
- Every structure of UniProt P15308
- Elsewhere: RCSB PDB 7KBF · PDBe 7KBF · UniProt P84233 · UniProt P62799 · UniProt Q6DKE3 · UniProt P02281 · UniProt P15308
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