Research workbench
Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122
Analyse Crystal structure of the nucleosome containing histone H3 with the crotonylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B0Y
- Type
- protein + DNA
- Length
- 1,043 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)
- UniProt
- Q71DI3, P62805, P04908, P06899
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 96 | 66% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 105 | 56% helix, 7% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
| E | Histone H3.2 | protein | 99 | 66% helix, 4% strand | Q71DI3 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 57% helix, 7% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains E, I, J
- CL · Chloride ion · ion · 2 copies · chains C, D, J, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.80 | 0.83 | 74 | empty |
| 2 | 485 | 0.77 | 0.85 | 45 | empty |
| 3 | 490 | 0.76 | 0.85 | 45 | empty |
| 4 | 810 | 0.70 | 0.77 | 56 | empty |
| 5 | 166 | 0.66 | 0.87 | 31 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6461 Ų buried · 631 hydrogen bonds · nucleic-nucleic
- E–F · 2669 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2631 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2623 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2554 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5B0Y · Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 · the same entry in another collection · chain J against J, TM-score 1.00
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 5B0Y · PDBe 5B0Y · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt P06899
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.