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Crystal structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8ACK12AC)

Analyse Crystal structure of the first bromodomain of human BRD4 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UW9
Type: protein
Length: 464 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 4; Histone H4
UniProt: O60885, P62805
Ligands: ALY
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 62% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 4	protein	124	58% helix, 0% strand	O60885
B	Bromodomain-containing protein 4	protein	109	66% helix, 0% strand	O60885
C	Bromodomain-containing protein 4	protein	112	63% helix, 0% strand	O60885
D	Bromodomain-containing protein 4	protein	109	66% helix, 0% strand	O60885
E	Histone H4	protein	4	0% helix, 0% strand	P62805
F	Histone H4	protein	6	0% helix, 0% strand	P62805

Ligands and binding sites

ALY · N(6)-acetyllysine · ligand · chains C, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	831	0.75	0.79	50	empty
2	214	0.62	0.82	30	ALY
3	168	0.50	0.77	23	empty
4	147	0.48	0.77	26	empty
5	117	0.39	0.74	20	empty

Interfaces

9 interfaces between chains.

C–D · 419 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 410 Å² buried · 5 hydrogen bonds · protein-protein
B–F · 386 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 363 Å² buried · 2 hydrogen bonds · protein-protein
D–F · 361 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 1 covalent (acetylation, covalent ligand).

Compared structures

3UW9 · Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated… · the same entry in another collection · chain F against F, TM-score 1.00
O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain D against A, TM-score 0.98
P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain F against A, TM-score 0.56

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
Every structure of UniProt P62805
Elsewhere: RCSB PDB 3UW9 · PDBe 3UW9 · UniProt O60885 · UniProt P62805

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