MolNFT v1 · #141277 · protein + DNA
Crystal structure of the nucleosome containing a chimeric histone H3/CENP-a catd
5Z23 · Histone H3.1,HISTONE H3-like centromeric protein A,HISTONE…: “Crystal structure of the nucleosome containing a chimeric histone H3/CENP-a catd”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #141277 on GenesisL1…
- PDB
- 5Z23
- Type
- protein + DNA
- Length
- 1,047 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1,HISTONE H3-like centromeric protein A,HISTONE H3.1; Histone H4; Histone H2A…
- UniProt
- P68431, P49450, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1,HISTONE H3-like centromeric protein A,HISTONE H3.1 | protein | 99 | 67% helix, 4% strand | P68431, P49450 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 106 | 58% helix, 7% strand | P04908 |
| D | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| E | Histone H3.1,HISTONE H3-like centromeric protein A,HISTONE H3.1 | protein | 100 | 66% helix, 4% strand | P68431, P49450 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 59% helix, 7% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| I, J | DNA (146-mer) | 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 | 574 | 0.80 | 0.86 | 71 | empty |
| 2 | 406 | 0.77 | 0.86 | 52 | empty |
| 3 | 377 | 0.75 | 0.86 | 54 | empty |
| 4 | 741 | 0.74 | 0.80 | 50 | empty |
| 5 | 198 | 0.67 | 0.86 | 32 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6364 Ų buried · 537 hydrogen bonds · nucleic-nucleic
- G–H · 2651 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2545 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2507 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5Z23 · Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD · the same entry in another collection · chain J against J, TM-score 1.00
- P49450 · AlphaFold monomer V2.0 prediction for histone H3-like centromeric protein a (P49450) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P49450
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 5Z23 · PDBe 5Z23 · UniProt P68431 · UniProt P49450 · UniProt P62805 · UniProt P04908 · UniProt P06899
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.