Research workbench
The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure
Analyse The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C1B
- Type
- protein + DNA
- Length
- 1,054 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like; Histone H4; Histone H2A type 1; Histone 2, H2BF; Palindromic 146BP human…
- UniProt
- P02302, P62799, P06897, Q28D68
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3-like | protein | 98 | 65% helix, 4% strand | P02302 |
| B | Histone H4 | protein | 80 | 61% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 106 | 57% helix, 7% strand | P06897 |
| D | Histone 2, H2BF | protein | 95 | 73% helix, 4% strand | Q28D68 |
| E | Histone H3-like | protein | 99 | 66% helix, 4% strand | P02302 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
| G | Histone H2A type 1 | protein | 103 | 57% helix, 6% strand | P06897 |
| H | Histone 2, H2BF | protein | 94 | 73% helix, 4% strand | Q28D68 |
| I, J | Palindromic 146BP human alpha satellite DNA | dna | 146 | — | — |
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 | 419 | 0.76 | 0.86 | 53 | empty |
| 2 | 274 | 0.75 | 0.89 | 37 | empty |
| 3 | 659 | 0.67 | 0.76 | 46 | empty |
| 4 | 546 | 0.66 | 0.77 | 52 | empty |
| 5 | 235 | 0.66 | 0.84 | 29 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6354 Ų buried · 499 hydrogen bonds · nucleic-nucleic
- C–D · 2606 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2581 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2579 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2544 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3C1B · The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin… · the same entry in another collection · chain J against J, TM-score 1.00
- P02302 · AlphaFold monomer V2.0 prediction for histone H3.3C (P02302) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P02302
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt Q28D68
- Elsewhere: RCSB PDB 3C1B · PDBe 3C1B · UniProt P02302 · UniProt P62799 · UniProt P06897 · UniProt Q28D68
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