Research workbench
Crystal structure of the BCL6 btb-domain with compound 1
Analyse Crystal structure of the BCL6 btb-domain with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MW6
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-cell lymphoma 6 protein
- UniProt
- P41182
- Ligands
- RC0
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-cell lymphoma 6 protein | protein | 122 | 52% helix, 15% strand | P41182 |
| B | B-cell lymphoma 6 protein | protein | 119 | 53% helix, 15% strand | P41182 |
Ligands and binding sites
- RC0 · 5-chloranyl-~{N}-(4-chlorophenyl)-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-amine · ligand · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.48 | 0.78 | 23 | RC0 |
| 2 | 107 | 0.42 | 0.77 | 17 | empty |
| 3 | 50 | 0.33 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1778 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 5MW6 · PDBe 5MW6 · UniProt P41182
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