Research workbench

BRD3-BD1 in complex with the cyclic peptide 3.1_3

Analyse BRD3-BD1 in complex with the cyclic peptide 3.1_3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U4A
Type: protein
Length: 266 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 3; Cyclic peptide 3.1_3
UniProt: Q15059
Ligands: ACE, NH2, SO4
Pockets: 5 · best druggability 0.36

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 3	protein	120	56% helix, 2% strand	Q15059
B	Bromodomain-containing protein 3	protein	124	54% helix, 2% strand	Q15059
D, C	Cyclic peptide 3.1_3	protein	11	0% helix, 45% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains B, D, A, C
NH2 · Amino group · ion · 2 copies · chains D, C
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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	81	0.36	0.76	15	empty
2	51	0.35	0.79	16	empty
3	74	0.34	0.76	18	empty
4	62	0.32	0.76	15	empty
5	53	0.31	0.76	11	empty

Interfaces

3 interfaces between chains.

A–B · 994 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 590 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 580 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, acetylation).

Compared structures

6U4A · BRD3-BD1 in complex with the cyclic peptide 3.1_3 · the same entry in another collection · chain A against A, TM-score 1.00
Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q15059
Elsewhere: RCSB PDB 6U4A · PDBe 6U4A · UniProt Q15059

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