Research workbench
Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
Analyse Crystal structure of the complex of human chromobox homolog 3 (CBX3) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DM1
- Type
- protein
- Length
- 244 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Chromobox protein homolog 3; Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
- UniProt
- Q13185, Q96KQ7
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · resolution 2.4 · 6 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chromobox protein homolog 3 | protein | 52 | 29% helix, 48% strand | Q13185 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | protein | 8 | 0% helix, 25% strand | Q96KQ7 |
| D | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | protein | 10 | 0% helix, 10% strand | Q96KQ7 |
| E, G | Chromobox protein homolog 3 | protein | 53 | 23% helix, 43% strand | Q13185 |
| F | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | protein | 9 | 0% helix, 22% strand | Q96KQ7 |
| H | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 | protein | 7 | 0% helix, 29% strand | Q96KQ7 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.66 | 0.95 | 19 | empty |
| 2 | 102 | 0.35 | 0.74 | 17 | empty |
| 3 | 86 | 0.35 | 0.74 | 18 | empty |
Interfaces
18 interfaces between chains.
- A–B · 601 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 600 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 579 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 569 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 490 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (methylation, disulfide).
Compared structures
- 3DM1 · Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide · the same entry in another collection · chain H against H, TM-score 1.00
- Q13185 · AlphaFold monomer V2.0 prediction for chromobox protein homolog 3 (Q13185) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 Q13185
- Every structure of UniProt Q96KQ7
- Elsewhere: RCSB PDB 3DM1 · PDBe 3DM1 · UniProt Q13185 · UniProt Q96KQ7
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