5DKD Hydrolase date Sep 03, 2015
title Crystal Structure Of The Bromodomain Of Human Brg1 (Smarca4) Complex With Pfi-3 Chemical Probe
authors C.Tallant, D.R.Owen, B.S.Gerstenberger, O.Fedorov, P.Savitsky, G. Alonso, J.A.Newman, P.Filippakopoulos, N.Burgess-Brown, F.Von D C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Muller, S.Knapp
compound source
Molecule: Transcription Activator Brg1
Chain: A, B
Fragment: Unp Residues 1418-1536
Synonym: Atp-Dependent Helicase Smarca4,Brg1-Associated Fac Baf190a,Mitotic Growth And Transcription Activator,Protein Protein Brahma Homolog 1,Snf2-Beta,Swisnf-Related Matrix-A Actin-Dependent Regulator Of Chromatin Subfamily A Member 4
Ec: 3.6.4.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Smarca4, Baf190a, Brg1, Snf2b, Snf2l4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 1 21 1
R_factor 0.268 R_Free 0.297
length a length b length c angle alpha angle beta angle gamma
45.926 74.566 52.626 90.00 109.90 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 5BW, EDO, ZN enzyme Hydrolase E.C.3.6.4 BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (5dkd.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (5dkd.pdb2.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 5DKD
  • CSU: Contacts of Structural Units for 5DKD
  • Structure Factors (402 Kb)
  • Retrieve 5DKD in mmCIF format [Save to disk]
  • Re-refined 5dkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DKD 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 5DKD
  • 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
  • Fold representative 5dkd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dkd_A] [5dkd_B] [5dkd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DKD: [BROMO ] by SMART
  • Other resources with information on 5DKD
  • Community annotation for 5DKD at PDBWiki (http://pdbwiki.org)

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