5D7X: Human BRPF1 bromodomain

Crystal structure of the human BRPF1 bromodomain in complex with XZ08. Determined by X-ray diffraction at 1.35 Å resolution. Released 25 May 2016.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,285
Mol. weight: 14.02 kDa
Ligands: XZ8
Released: 25 May 2016

Explore 5D7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D7X contains 5 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	630-647	18
α-helix	665-668	4
α-helix	675-683	9
α-helix	690-707	18
α-helix	713-737	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peregrin	A	protein	116	Homo sapiens	P55201 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5D7X_1 Peregrin (chains A)
SMEMQLTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEA
YRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEKMG

Ligands and cofactors

ID	Name	Formula	Copies
XZ8	4-(1-acetyl-1H-indol-3-yl)-5-methyl-1,2-dihydro-3H-pyrazol-3-one	C14 H13 N3 O2	1

Water and common crystallization additives (NO3) are not listed.

Primary citation

The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. Unzue, A., Zhao, H., Lolli, G. et al. J Med Chem (2016) 59:3087-3097. DOI 10.1021/acs.jmedchem.5b01757 · PubMed

Other PDB entries of the same protein (UniProt P55201 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MWZ 1.25 Å, Crystal structure of the human BRPF1 bromodomain in complex with BZ073
3L42 1.3 Å, PWWP domain of human bromodomain and PHD finger containing protein 1
5C6S 1.3 Å, Human Bromodomain and PHD Finger Containing 1, PWWP domain in complex with XST005904a
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
5O5F 1.3 Å, Crystal structure of the human BRPF1 bromodomain in complex with BZ038
5ETB 1.33 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED13
7C4I 1.37 Å, High resolution structure of BRPF1 Bromo Domain from Biortus
5EM3 1.4 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED9
5ETD 1.4 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED14
8QAZ 1.4 Å, Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative…
8QB2 1.42 Å, Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative…
5EV9 1.45 Å, Crystal structure of the human BRPF1 bromodomain in complex with SEED15

Browse structure collections

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