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 Diffractionresolution 1.80 Å
ligand ALY, SO4 enzyme
Primary referenceStructural 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
  • Other resources with information on 4QYL
  • Community annotation for 4QYL at PDBWiki (http://pdbwiki.org)

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