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Crystal structure of the BCL6 btb domain in complex with pyrazolo- pyrimidine ligand

Analyse Crystal structure of the BCL6 btb domain in complex with pyrazolo- pyrimidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N1X
Type: protein
Length: 481 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-cell lymphoma 6 protein
UniProt: P41182
Ligands: 8HH
Pockets: 5 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B-cell lymphoma 6 protein	protein	121	54% helix, 15% strand	P41182
B, C	B-cell lymphoma 6 protein	protein	121	57% helix, 15% strand	P41182
D	B-cell lymphoma 6 protein	protein	118	56% helix, 15% strand	P41182

Ligands and binding sites

8HH · ~{N}-ethyl-5-pyridin-3-yl-pyrazolo[1,5-a]pyrimidin-7-amine · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.44	0.77	21	8HH
2	112	0.43	0.77	19	empty
3	113	0.40	0.76	19	empty
4	88	0.39	0.77	18	empty
5	83	0.29	0.72	16	empty

Interfaces

3 interfaces between chains.

C–D · 1844 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1843 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 67 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5N1X · Crystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine ligand · the same entry in another collection · chain D against D, 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 0.36

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 5N1X · PDBe 5N1X · UniProt P41182

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