MolNFT v1 · #179627 · protein + DNA
H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract (oligo fraction)
7KBF · Histone H3.2: “H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract (oligo fraction)”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #179627 on GenesisL1: 3D structure, binding sites…
- 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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