MolNFT v1 · #166844 · protein + DNA
The nucleosome structure after H2A-H2B exchange
6V2K · Histone H3.1: “The nucleosome structure after H2A-H2B exchange”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #166844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V2K
- Type
- protein + DNA
- Length
- 1,042 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A; Histone H2B type 1-J; DNA (146-mer)
- UniProt
- P68431, P62805, Q08AJ9, P06899
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 96 | 67% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 77 | 64% helix, 9% strand | P62805 |
| C | Histone H2A | protein | 108 | 56% helix, 6% strand | Q08AJ9 |
| D | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 63% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| G | Histone H2A | protein | 104 | 58% helix, 7% strand | Q08AJ9 |
| H | Histone H2B type 1-J | protein | 91 | 75% helix, 4% strand | P06899 |
| I | DNA (146-mer) | dna | 145 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 10 copies · chains E, F, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 782 | 0.80 | 0.83 | 78 | empty |
| 2 | 488 | 0.76 | 0.84 | 53 | empty |
| 3 | 348 | 0.74 | 0.86 | 50 | empty |
| 4 | 739 | 0.70 | 0.77 | 70 | empty |
| 5 | 601 | 0.67 | 0.77 | 37 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6391 Ų buried · 534 hydrogen bonds · nucleic-nucleic
- E–F · 2672 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2589 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2509 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6V2K · The nucleosome structure after H2A-H2B exchange · the same entry in another collection · chain J against J, TM-score 1.00
- 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
- 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
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 Q08AJ9
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6V2K · PDBe 6V2K · UniProt P68431 · UniProt P62805 · UniProt Q08AJ9 · UniProt P06899
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