4QYL	Protein Binding	date	Jul 24, 2014
title	Crystal Structure Of The Human Brpf1 Bromodomain In Complex Histone H2ak5ac Peptide
authors	M.Y.Lubula, K.C.Glass
compound		source
Molecule: Peregrin Chain: A, B, C, D Fragment: Bromodomain (Unp Residues 629-742) Synonym: Bromodomain And Phd Finger-Containing Protein 1, P Br140; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Br140, Brpf1 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Rosetta2de3plyss Expression_system_vector_type: Plasmid Expression_system_plasmid: Pdest15
Molecule: Histone H2a Type 1 Chain: E, F, G, H Fragment: Histone H2ak5ac Peptide (Unp Residues 2-13) Synonym: H2a.1, Histone H2ap Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606
symmetry	Space Group: P 1 21 1	R_factor 0.204 R_Free 0.253
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.908 55.581 82.135 90.00 93.58 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	ALY, SO4	enzyme
Primary reference	Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain., Lubula MY, Eckenroth BE, Carlson S, Poplawski A, Chruszcz M, Glass KC, FEBS Lett. 2014 Sep 30. pii: S0014-5793(14)00705-4. doi:, 10.1016/j.febslet.2014.09.028. PMID:25281266

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk] Biological Unit Coordinates (4qyl.pdb1.gz) 26 Kb Biological Unit Coordinates (4qyl.pdb2.gz) 27 Kb Biological Unit Coordinates (4qyl.pdb3.gz) 27 Kb Biological Unit Coordinates (4qyl.pdb4.gz) 26 Kb LPC: Ligand-Protein Contacts for 4QYL CSU: Contacts of Structural Units for 4QYL Structure Factors (970 Kb) Retrieve 4QYL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4QYL from S2C, [Save to disk] Re-refined 4qyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4QYL in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 4QYL

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 4QYL, from MSDmotif at EBI Fold representative 4qyl from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4qyl_H] [4qyl_E] [4qyl_B] [4qyl_G] [4qyl_D] [4qyl_A] [4qyl_F] [4qyl_C] [4qyl] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 4QYL: [BROMO ] by SMART

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