MolNFT v1 · #145853 · protein
Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9ME3 peptide
6D07 · Chromobox protein homolog 1: “Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9ME3 peptide”. X-ray diffraction, 1 pocket (best druggability 0.36). MolNFT v1 #145853 on GenesisL1: 3D structure…
- PDB
- 6D07
- Type
- protein
- Length
- 122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromobox protein homolog 1; Histone H3.1
- UniProt
- P83916, P68431
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromobox protein homolog 1 | protein | 54 | 31% helix, 50% strand | P83916 |
| B | Chromobox protein homolog 1 | protein | 52 | 27% helix, 52% strand | P83916 |
| C | Histone H3.1 | protein | 9 | 0% helix, 33% strand | P68431 |
| D | Histone H3.1 | protein | 7 | 0% helix, 43% strand | P68431 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.36 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 662 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 321 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6D07 · Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3… · the same entry in another collection · chain A against A, TM-score 1.00
- P83916 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 1 (P83916) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P83916
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 6D07 · PDBe 6D07 · UniProt P83916 · UniProt P68431
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