4YOS Transcription date Mar 12, 2015
title P107 Pocket Domain Complexed With Lin52 Peptide
authors K.Z.Guiley, T.J.Liban, J.G.Felthousen, P.Ramanan, S.Tripathi, L.Litovchick, S.M.Rubin
compound source
Molecule: Retinoblastoma-Like Protein 1,Retinoblastoma-Like 1;
Chain: A
Fragment: Unp Residues 391-600,Unp Residues 781-969,Unp Res 600,Unp Residues 781-969;
Synonym: 107 Kda Retinoblastoma-Associated Protein,P107,Prb
Engineered: Yes
Organism_scientific: Homo Sapiens, Myotis Davidii
Organism_common: Human, David'S Myotis
Organism_taxid: 9606, 225400
Gene: Rbl1, Mda_glean10022721
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protein Lin-52 Homolog
Chain: E
Fragment: Unp Residues 15-34
Engineered: Yes

Synthetic: Yes
Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
symmetry Space Group: C 2 2 21
R_factor 0.199 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
75.430 101.060 140.685 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand EDO, SEP, SO4 enzyme
Gene MDA


Primary referenceStructural mechanisms of DREAM complex assembly and regulation., Guiley KZ, Liban TJ, Felthousen JG, Ramanan P, Litovchick L, Rubin SM, Genes Dev. 2015 May 1;29(9):961-74. doi: 10.1101/gad.257568.114. Epub 2015 Apr, 27. PMID:25917549
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (4yos.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 4YOS
  • CSU: Contacts of Structural Units for 4YOS
  • Structure Factors (1445 Kb)
  • Retrieve 4YOS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YOS from S2C, [Save to disk]
  • Re-refined 4yos structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YOS 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 4YOS
  • 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 4YOS, from MSDmotif at EBI
  • Fold representative 4yos from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yos_A] [4yos] [4yos_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YOS: [CYCLIN] [RB_A ] by SMART
  • Other resources with information on 4YOS
  • Community annotation for 4YOS at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science