9KEM | pdb_00009kem

Crystal structure of BRD4-BD1 in complex with H2AK5acK9ac

• PDB DOI: https://doi.org/10.2210/pdb9KEM/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-05 Released: 2026-06-10 
• Deposition Author(s): Wang, X.D., Ji, J.H., Yang, H.W., Li, Z.B., Yang, N.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Crystal structure of BRD4-BD1 in complex with H2AK5acK9ac

Wang, X.D., Yang, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A8B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A8B1C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 56.99 kDa 
• Atom Count: 4,060 
• Modeled Residue Count: 435 
• Deposited Residue Count: 475 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B, C, D	115	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H2A(1-15)	E	15	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	E	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.968	α = 90
b = 79.592	β = 92.784
c = 65.141	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Wang, X.D., Ji, J.H., Yang, H.W., Li, Z.B., Yang, N.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0508902
National Natural Science Foundation of China (NSFC)	China	32170549

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release