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Crystal structure of the BCL6 btb domain dimer in complex with the bcor bbd corepressor peptide

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

PDB: 3BIM
Type: protein
Length: 1,121 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: B-cell lymphoma 6 protein; BCL-6 corepressor
UniProt: P41182, Q6W2J9
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	B-cell lymphoma 6 protein	protein	125	50% helix, 17% strand	P41182
I, J, K, M, O, P	BCL-6 corepressor	protein	17	0% helix, 24% strand	Q6W2J9
B, D	B-cell lymphoma 6 protein	protein	124	48% helix, 18% strand	P41182
L, N	BCL-6 corepressor	protein	16	0% helix, 25% strand	Q6W2J9
E	B-cell lymphoma 6 protein	protein	123	47% helix, 16% strand	P41182
F	B-cell lymphoma 6 protein	protein	122	50% helix, 16% strand	P41182
G	B-cell lymphoma 6 protein	protein	122	51% helix, 17% strand	P41182
H	B-cell lymphoma 6 protein	protein	122	49% helix, 17% strand	P41182

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.79	0.81	85	empty
2	192	0.58	0.80	30	empty
3	245	0.55	0.77	27	empty
4	222	0.54	0.78	28	empty
5	228	0.52	0.76	30	empty

Interfaces

33 interfaces between chains.

A–B · 2066 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2046 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1965 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 1936 Å² buried · 30 hydrogen bonds · protein-protein
I–B · 712 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3BIM · Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor… · the same entry in another collection · chain F against F, TM-score 1.00

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
Every structure of UniProt Q6W2J9
Elsewhere: RCSB PDB 3BIM · PDBe 3BIM · UniProt P41182 · UniProt Q6W2J9

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