4YYD: BRD9 Bromodomain

Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide. Determined by X-ray diffraction at 1.52 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,040
Mol. weight: 13.55 kDa
Released: 16 Sept 2015

Explore 4YYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YYD contains 6 α-helices and 0 β-strands across 1 chain. 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	26-38	13
α-helix	48-50	3
α-helix	57-60	4
α-helix	67-75	9
α-helix	82-99	18
α-helix	105-121	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 9	A	protein	108	Homo sapiens	Q9H8M2 (AlphaFold model)
Histone H4	Z	protein	11	Homo sapiens	P62805 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YYD_1 Bromodomain-containing protein 9 (chains A)
GSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIV
ANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK

Sequence of entity 2 (Z), FASTA

>4YYD_2 Histone H4 (chains Z)
SGRGXGGXGLG

Primary citation

A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Flynn, E.M., Huang, O.W., Poy, F. et al. Structure (2015) 23:1801-1814. DOI 10.1016/j.str.2015.08.004 · PubMed

Other PDB entries of the same protein (UniProt Q9H8M2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BQA 1.03 Å, BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]…
5I40 1.04 Å, BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)
9ZU4 1.05 Å, Crystal structure of BRD9 bromodomain bound to BZ2
9ZU3 1.15 Å, Crystal structure of BRD9 bromodomain bound to BZ1
5I7X 1.18 Å, BRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]py…
6Y7K 1.2 Å, Structure of the BRD9 bromodomain and compound 27
4UIT 1.3 Å, BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-dimethoxyphenyl)-2-(4-…
6V1B 1.35 Å, Crystal structure of the bromodomain of human BRD9 bound to I-BRD9
5JI8 1.42 Å, Crystal structure of the BRD9 bromodomain and hit 1
4YY6 1.45 Å, Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide
5I7Y 1.45 Å, BRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]py…
4YY4 1.47 Å, Crystal structure of BRD9 Bromodomain bound to DMSO

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