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
crystal
cell
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
Gene
Ontology
ChainFunctionProcessComponent
A


E


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)

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