Research workbench
Crystal structure of the BCL6 btb domain in complex with an APT48 peptide
Analyse Crystal structure of the BCL6 btb domain in complex with an APT48 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TBT
- Type
- protein
- Length
- 258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-cell lymphoma 6 protein; APT48 peptide
- UniProt
- P41182
- Ligands
- MG, NA, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | B-cell lymphoma 6 protein | protein | 123 | 56% helix, 15% strand | P41182 |
| C, D | APT48 peptide | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 152 | 0.52 | 0.80 | 23 | CL |
| 2 | 101 | 0.50 | 0.81 | 20 | CL |
| 3 | 57 | 0.27 | 0.74 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1844 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 329 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 262 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TBT · Crystal structure of the BCL6 BTB domain in complex with an Apt48 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P41182 · AlphaFold monomer V2.0 prediction for B-cell lymphoma 6 protein (P41182) · a predicted model of the same protein · chain A against A, TM-score 0.31
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 P41182
- Elsewhere: RCSB PDB 6TBT · PDBe 6TBT · UniProt P41182
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