2YED Chaperone date Mar 25, 2011
title Hsp90 Inhibitors And Drugs From Fragment And Virtual Screening
authors S.D.Roughley, R.E.Hubbard, L.M.Baker
compound source
Molecule: Heat Shock Protein Hsp 90-Alpha
Chain: A
Fragment: N-Terminal Atp-Binding Domain, Residues 9-236
Synonym: Heat Shock 86 Kda, Hsp 86, Hsp86, Renal Carcinoma Ny-Ren-38;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Skin
Tissue: Melanoma
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet19
symmetry Space Group: I 2 2 2
R_factor 0.20564 R_Free 0.25778
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.326 89.194 99.888 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand ADE, CL BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHow Well Can Fragments Explore Accessed Chemical Space? A Case Study from Heat Shock Protein 90., Roughley SD, Hubbard RE, J Med Chem. 2011 May 24. PMID:21561141
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (2yed.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2YED
  • CSU: Contacts of Structural Units for 2YED
  • Structure Factors (859 Kb)
  • Retrieve 2YED in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YED from S2C, [Save to disk]
  • Re-refined 2yed structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YED 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 2YED
  • 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 2YED, from MSDmotif at EBI
  • Fold representative 2yed from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yed_A] [2yed]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YED: [HATPase_c ] by SMART
  • Alignments of the sequence of 2YED with the sequences similar proteins can be viewed for 2YED's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2YED
  • Community annotation for 2YED at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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