4X3T: Chromobox protein homolog 7
Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452. Determined by X-ray diffraction at 2.14 Å resolution. Released 4 Mar 2015.
- Method
- X-ray diffraction
- Resolution
- 2.14 Å
- Organism
- Mus musculus
- Chains
- 6
- Atoms
- 3,508
- Mol. weight
- 49.43 kDa
- Ligands
- ZN, 45E
- Released
- 4 Mar 2015
Explore 4X3T in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4X3T contains 21 α-helices and 22 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-22 | 10 | 1 |
| β-strand | 25-32 | 8 | 1 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 1 |
| α-helix | 45-47 | 3 | |
| α-helix | 51-61 | 11 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-22 | 10 | 2 |
| β-strand | 25-32 | 8 | 2 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 2 |
| α-helix | 45-47 | 3 | |
| α-helix | 51-62 | 12 | |
Chain C: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-11 | 2 | |
| β-strand | 13-22 | 10 | 3 |
| β-strand | 25-32 | 8 | 3 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 3 |
| α-helix | 45-47 | 3 | |
| α-helix | 51-61 | 11 | |
Chain D: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| β-strand | 10 | 1 | 4 |
| β-strand | 13-22 | 10 | 5 |
| β-strand | 25-32 | 8 | 5 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 5 |
| α-helix | 45-48 | 4 | |
| β-strand | 49 | 1 | 6 |
| α-helix | 51-59 | 9 | |
Chain E: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| β-strand | 10 | 1 | 6 |
| β-strand | 13-22 | 10 | 7 |
| β-strand | 25-32 | 8 | 7 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 7 |
| α-helix | 45-48 | 4 | |
| β-strand | 49 | 1 | 4 |
| α-helix | 51-53 | 3 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-22 | 10 | 8 |
| β-strand | 25-32 | 8 | 8 |
| α-helix | 37-39 | 3 | |
| β-strand | 41-44 | 4 | 8 |
| α-helix | 45-47 | 3 | |
| α-helix | 52-57 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromobox protein homolog 7 | A, B, C, D, E, F | protein | 64 | Mus musculus | Q8VDS3 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>4X3T_1 Chromobox protein homolog 7 (chains A, B, C, D, E, F)
GSHMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
RDRA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 9 |
| 45E | 1-[4-(2,3-dimethoxybenzoyl)piperazin-1-yl]-2-(3-methylphenoxy)ethanone | C22 H26 N2 O5 | 6 |
Water and common crystallization additives (EDO) are not listed.
Primary citation
Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Ren, C., Morohashi, K., Plotnikov, A.N. et al. Chem Biol (2015) 22:161-168. DOI 10.1016/j.chembiol.2014.11.021 · PubMed
Other PDB entries of the same protein (UniProt Q8VDS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4X3K 1.45 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27me3 peptide
- 4X3S 1.6 Å, Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide
- 4X3U 1.63 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with Suramin
- 5EJW 2.6 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS351
- 2KVM Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide
Browse structure collections
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