Research workbench
Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MEK4
Analyse Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B2V
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromodomain-helicase-DNA-binding protein 1; Histone H3
- UniProt
- O14646, P68431
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromodomain-helicase-DNA-binding protein 1 | protein | 175 | 43% helix, 22% strand | O14646 |
| B | Chromodomain-helicase-DNA-binding protein 1 | protein | 170 | 41% helix, 22% strand | O14646 |
| C | Chromodomain-helicase-DNA-binding protein 1 | protein | 85 | 33% helix, 28% strand | O14646 |
| D | Histone H3 | protein | 6 | 0% helix, 0% strand | P68431 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.85 | 0.86 | 102 | empty |
| 2 | 144 | 0.48 | 0.78 | 21 | empty |
| 3 | 97 | 0.47 | 0.81 | 19 | empty |
| 4 | 92 | 0.45 | 0.80 | 17 | empty |
| 5 | 132 | 0.43 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1399 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 484 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 244 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 2B2V · Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi… · the same entry in another collection · chain D against D, TM-score 1.00
- O14646 · AlphaFold monomer V2.0 prediction for chromodomain-helicase-DNA- binding protein 1… · 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 O14646
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 2B2V · PDBe 2B2V · UniProt O14646 · UniProt P68431
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