MolNFT v1 · #62075 · protein

Crystal structure of the wild-type human BCL6 BTB/POZ domain

3E4U · B-cell lymphoma 6 protein: “Crystal structure of the wild-type human BCL6 BTB/POZ domain”. X-ray diffraction, 14 pockets (best druggability 0.69). MolNFT v1 #62075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3E4U
Type: protein
Length: 698 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-cell lymphoma 6 protein
UniProt: P41182
Pockets: 14 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	B-cell lymphoma 6 protein	protein	119	55% helix, 12% strand	P41182
B	B-cell lymphoma 6 protein	protein	120	57% helix, 12% strand	P41182
D	B-cell lymphoma 6 protein	protein	118	53% helix, 14% strand	P41182
E	B-cell lymphoma 6 protein	protein	112	55% helix, 15% strand	P41182
F	B-cell lymphoma 6 protein	protein	110	58% helix, 16% strand	P41182

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	769	0.69	0.76	58	empty
2	707	0.69	0.77	68	empty
3	268	0.61	0.80	38	empty
4	156	0.56	0.81	24	empty
5	160	0.54	0.80	23	empty

Interfaces

11 interfaces between chains.

A–B · 1757 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1739 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1659 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 301 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 288 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3E4U · Crystal Structure of the Wild-Type Human BCL6 BTB/POZ Domain · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.38

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 3E4U · PDBe 3E4U · UniProt P41182

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