Research workbench
Cryo-EM structure of nucleosome core particle composed of the widom 601 DNA sequence
Analyse Cryo-EM structure of nucleosome core particle composed of the widom 601 DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OHC
- Type
- protein + DNA
- Length
- 1,054 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 (145-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 68% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 56% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 109 | 53% helix, 6% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 97 | 72% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 98 | 63% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 80 | 65% helix, 9% strand | P62799 |
| G | Histone H2A | protein | 106 | 57% helix, 7% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 75% helix, 4% strand | P02281 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.81 | 0.84 | 71 | empty |
| 2 | 413 | 0.74 | 0.84 | 52 | empty |
| 3 | 387 | 0.73 | 0.84 | 46 | empty |
| 4 | 900 | 0.72 | 0.77 | 85 | empty |
| 5 | 172 | 0.71 | 0.90 | 33 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6501 Ų buried · 513 hydrogen bonds · nucleic-nucleic
- G–H · 2615 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2595 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2579 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2536 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7OHC · Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence · the same entry in another collection · chain J against J, 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 0.99
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 7OHC · PDBe 7OHC · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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