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BRD4-BD1 in complex with the cyclic peptide 3.2_1

Analyse BRD4-BD1 in complex with the cyclic peptide 3.2_1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U8M
Type: protein
Length: 252 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 4; Cyclic peptide 3.2_1
UniProt: O60885
Ligands: ACE, NH2
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 4	protein	125	54% helix, 0% strand	O60885
B	Bromodomain-containing protein 4	protein	110	60% helix, 0% strand	O60885
C	Cyclic peptide 3.2_1	protein	17	0% helix, 59% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains B, C
NH2 · Amino group · ion · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.58	0.76	39	empty
2	89	0.49	0.82	17	empty

Interfaces

2 interfaces between chains.

B–C · 514 Å² buried · 1 hydrogen bond · protein-protein
A–B · 484 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, acetylation).

Compared structures

6U8M · BRD4-BD1 in complex with the cyclic peptide 3.2_1 · the same entry in another collection · chain A against A, TM-score 1.00
O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O60885
Elsewhere: RCSB PDB 6U8M · PDBe 6U8M · UniProt O60885

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