MolNFT v1 · #164863 · protein
Crystal structure of the BCL6 btb domain in complex with an APT48 peptide
6TBT · B-cell lymphoma 6 protein: “Crystal structure of the BCL6 btb domain in complex with an APT48 peptide”. X-ray diffraction, 3 ligands (MG, NA, CL), 3 pockets (best druggability 0.52). MolNFT v1 #164863 on GenesisL1: 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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