9MXK | pdb_00009mxk

BRD4-BD1 in complex with cyclic peptide 4.1C

PDB DOI: https://doi.org/10.2210/pdb9MXK/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-20 Released: 2026-04-22
Deposition Author(s): Patel, K., Pachl, P., Mackay, J.P.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.213 (Depositor), 0.228 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

BRD4-BD1 in complex with cyclic peptide 4.1C

Patel, K., Mackay, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 54.43 kDa
Atom Count: 3,504
Modeled Residue Count: 410
Deposited Residue Count: 453
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, C [auth D], E [auth I]	133	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4.1C	B, D [auth E], F [auth J]	18	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain J [auth I] SDF format, chain I SDF format, chain H [auth D] SDF format, chain G [auth A] MOL2 format, chain J [auth I] MOL2 format, chain I MOL2 format, chain H [auth D] MOL2 format, chain G [auth A] mmCIF format, chain J [auth I] mmCIF format, chain I mmCIF format, chain H [auth D] mmCIF format, chain G [auth A]	G [auth A], H [auth D], I, J [auth I]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Focus chain I Focus chain J [auth I] Interactions & Density Focus chain G [auth A] Focus chain H [auth D] Focus chain I Focus chain J [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	B, D [auth E], F [auth J]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.213 (Depositor), 0.228 (DCC)
R-Value Work: 0.176 (Depositor), 0.190 (DCC)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.121	α = 90
b = 70.121	β = 90
c = 90.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2026-04-22
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.