Research workbench
Crystal structure of the human nucleosome containing H2A.Z.1 S42R
Analyse Crystal structure of the human nucleosome containing H2A.Z.1 S42R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JOU
- Type
- protein + DNA
- Length
- 1,041 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.17
- Source
- Homo sapiens
- Molecule
- Histone H3.1; Histone H4; Histone H2A.Z; Histone H2B type 1-J; DNA (146-mer)
- UniProt
- P68431, P62805, P0C0S5, P06899
- Ligands
- MN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.17 · 9 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 96 | 66% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 77 | 64% helix, 8% strand | P62805 |
| C | Histone H2A.Z | protein | 106 | 57% helix, 6% strand | P0C0S5 |
| D | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 67% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 84 | 60% helix, 7% strand | P62805 |
| G | Histone H2A.Z | protein | 102 | 57% helix, 6% strand | P0C0S5 |
| H | Histone H2B type 1-J | protein | 92 | 74% helix, 4% strand | P06899 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 9 copies · chains E, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.79 | 0.81 | 107 | empty |
| 2 | 561 | 0.70 | 0.79 | 50 | empty |
| 3 | 482 | 0.70 | 0.80 | 46 | empty |
| 4 | 996 | 0.69 | 0.74 | 68 | MN |
| 5 | 506 | 0.64 | 0.77 | 33 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6457 Ų buried · 537 hydrogen bonds · nucleic-nucleic
- C–D · 2635 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2607 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2605 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2496 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6JOU · Crystal structure of the human nucleosome containing H2A.Z.1 S42R · the same entry in another collection · chain J against J, TM-score 1.00
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain B 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S5
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6JOU · PDBe 6JOU · UniProt P68431 · UniProt P62805 · UniProt P0C0S5 · UniProt P06899
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.