Research workbench
Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452
Analyse Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X3T
- Type
- protein
- Length
- 353 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromobox protein homolog 7
- UniProt
- Q8VDS3
- Ligands
- 45E, ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Chromobox protein homolog 7 | protein | 62 | 27% helix, 35% strand | Q8VDS3 |
| B | Chromobox protein homolog 7 | protein | 60 | 30% helix, 37% strand | Q8VDS3 |
| E | Chromobox protein homolog 7 | protein | 51 | 27% helix, 47% strand | Q8VDS3 |
| F | Chromobox protein homolog 7 | protein | 56 | 21% helix, 39% strand | Q8VDS3 |
Ligands and binding sites
- 45E · 1-[4-(2,3-dimethoxybenzoyl)piperazin-1-yl]-2-(3-methylphenoxy)ethanone · ligand · 6 copies · chains A, B, C, F, D, E
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, F, D, E
- EDO · 1,2-ethanediol · additive · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.73 | 0.77 | 87 | 45E, ZN, EDO |
| 2 | 281 | 0.63 | 0.80 | 30 | 45E |
| 3 | 65 | 0.37 | 0.78 | 15 | ZN |
| 4 | 51 | 0.25 | 0.73 | 9 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1077 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 656 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 218 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4X3T · Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452 · the same entry in another collection · chain F against F, TM-score 1.00
- Q8VDS3 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 7 (Q8VDS3) · a predicted model of the same protein · chain F against A, TM-score 0.82
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 Q8VDS3
- Elsewhere: RCSB PDB 4X3T · PDBe 4X3T · UniProt Q8VDS3
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