9MPL | pdb_00009mpl

BRD2-BD1 in complex with cyclic peptide 2.1C-W11A

PDB DOI: https://doi.org/10.2210/pdb9MPL/pdb

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

Deposited: 2024-12-30 Released: 2026-04-08
Deposition Author(s): Patel, K., Mackay, J.P.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.268 (Depositor), 0.268 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.213 (Depositor)

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

BRD2-BD1 in complex with cyclic peptide 2.1C-W11A

Patel, K., Mackay, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 34.91 kDa
Atom Count: 2,168
Modeled Residue Count: 262
Deposited Residue Count: 300
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B	135	Homo sapiens	Mutation(s): 0 Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2.1C-W11A	C [auth G], D [auth C]	15	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.268 (Depositor), 0.268 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.992	α = 90
b = 77.992	β = 90
c = 57.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-08

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: 2026-04-08
Type: Initial release

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