2YJD Hormone Receptor Peptide date May 19, 2011
title Stapled Peptide Bound To Estrogen Receptor Beta
authors C.Phillips, L.R.Roberts, M.Schade, A.Bent, N.L.Davies, R.Moore, A.D.Pannifer, D.G.Brown, A.R.Pickford, S.L.Irving
compound source
Molecule: Estrogen Receptor Beta
Chain: A, B
Fragment: Ligand-Binding Domain, Residues 261-500
Synonym: Er-Beta, Nuclear Receptor Subfamily 3 Group A Memb
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Stapled Peptide
Chain: C, D

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: I 4
R_factor 0.2246 R_Free 0.2602
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.620 102.620 102.620 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand ACE, MK8, NH2, YJD enzyme
Primary referenceDesign and structure of stapled peptides binding to estrogen receptors., Phillips C, Roberts LR, Schade M, Bazin R, Bent A, Davies NL, Moore R, Pannifer AD, Pickford AR, Prior SH, Read CM, Scott A, Brown DG, Xu B, Irving SL, J Am Chem Soc. 2011 Jun 29;133(25):9696-9. Epub 2011 Jun 6. PMID:21612236
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (2yjd.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 2YJD
  • CSU: Contacts of Structural Units for 2YJD
  • Structure Factors (531 Kb)
  • Retrieve 2YJD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YJD from S2C, [Save to disk]
  • Re-refined 2yjd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YJD 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 2YJD
  • 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 2YJD, from MSDmotif at EBI
  • Fold representative 2yjd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yjd_C] [2yjd_D] [2yjd_B] [2yjd] [2yjd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YJD: [HOLI ] by SMART
  • Alignments of the sequence of 2YJD with the sequences similar proteins can be viewed for 2YJD'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 2YJD
  • Community annotation for 2YJD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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