9NN4: BET BRD3-BD1

BET BRD3-BD1 in complex with peptide 7.2. Determined by X-ray diffraction at 1.37 Å resolution. Released 11 Feb 2026.

Method: X-ray diffraction
Resolution: 1.37 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 2,533
Mol. weight: 31.2 kDa
Released: 11 Feb 2026

Explore 9NN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NN4 contains 19 α-helices and 4 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	1
α-helix	37-41	5
α-helix	42-47	6
α-helix	48-51	4
α-helix	54-59	6
α-helix	73-76	4
α-helix	83-91	9
α-helix	98-115	18
α-helix	121-138	18
β-strand	146	1	1

Chain B: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	2
α-helix	37-41	5
α-helix	42-47	6
α-helix	48-51	4
α-helix	54-59	6
α-helix	65-68	4
α-helix	73-76	4
α-helix	83-91	9
α-helix	98-115	18
α-helix	121-139	19
β-strand	146	1	2

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	89-91	3

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 3	A, B	protein	120	Homo sapiens	Q15059 (AlphaFold model)
peptide 7.2	D, E	protein	11	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9NN4_1 Bromodomain-containing protein 3 (chains A, B)
NPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIK
KRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVEL

Sequence of entity 2 (D, E), FASTA

>9NN4_2 peptide 7.2 (chains D, E)
XYQRKPRKLCX

Primary citation

The effect of peptide size on target affinity in mRNA display-derived macrocyclic peptides. Jing, X., Suh, J., Maxwell, J. et al. Chem Commun (Camb) (2026) 62:4028-4031. DOI 10.1039/d5cc06167a · PubMed

Other PDB entries of the same protein (UniProt Q15059 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QJU 1.2 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with…
3S92 1.36 Å, Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor…
2NXB 1.4 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3)
7TOA 1.41 Å, BRD3-BD1 in complex with RaPID linear peptide 3xAcK.1 (triAcK.1)
7LAY 1.45 Å, Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179
8CV5 1.47 Å, Peptide 4.2B in complex with BRD3.2
7L72 1.5 Å, Crystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280
7RJL 1.5 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
7TO8 1.5 Å, BRD3-BD1 in complex with RaPID linear peptide 2xAcK.1 (diAcK.1)
7L9L 1.55 Å, Crystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536
7TO9 1.6 Å, BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE)
9MPN 1.6 Å, BRD3-BD1 A128T mutant

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