MolNFT v1 · #59551 · protein + DNA
The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure
3C1B · Histone H3-like: “The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #59551 on GenesisL1: 3D structure, binding…
- 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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