Research workbench
Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9BN peptide
Analyse Crystal structure of an engineered bump-hole complex of mutant human chromobox… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D08
- Type
- protein
- Length
- 123 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
- Ligands
- SO4
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromobox protein homolog 1 | protein | 54 | 31% helix, 50% strand | P83916 |
| C | Histone H3.1 | protein | 8 | 0% helix, 38% strand | P68431 |
| B | Chromobox protein homolog 1 | protein | 52 | 29% helix, 52% strand | P83916 |
| D | Histone H3.1 | protein | 9 | 0% helix, 33% strand | P68431 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- B–D · 654 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 651 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 412 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6D08 · Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1… · 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 0.95
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 6D08 · PDBe 6D08 · UniProt P83916 · UniProt P68431
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