Research workbench
The human nucleosome structure containing the histone variant H3.2
Analyse The human nucleosome structure containing the histone variant H3.2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AV1
- 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; 146-mer DNA
- UniProt
- Q71DI3, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.81
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 | 67% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 105 | 57% helix, 7% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
| E | Histone H3.2 | protein | 99 | 64% helix, 4% strand | Q71DI3 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 56% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 76% helix, 4% strand | P06899 |
| I, J | 146-mer DNA | dna | 146 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.81 | 0.83 | 76 | empty |
| 2 | 397 | 0.77 | 0.87 | 49 | empty |
| 3 | 352 | 0.75 | 0.86 | 46 | empty |
| 4 | 923 | 0.73 | 0.77 | 69 | empty |
| 5 | 781 | 0.70 | 0.77 | 60 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6436 Ų buried · 509 hydrogen bonds · nucleic-nucleic
- E–F · 2631 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2615 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2594 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2537 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3AV1 · The human nucleosome structure containing the histone variant H3.2 · 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
- P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain H 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 3AV1 · PDBe 3AV1 · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt P06899
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