4YOZ Transcription date Mar 12, 2015
title P107 Pocket Domain In Complex With Hpv E7 Peptide
authors T.J.Liban, K.Z.Guiley, J.G.Felthousen, P.Ramanan, L.Litovchick, S
compound source
Molecule: Retinoblastoma-Like Protein 1,Retinoblastoma-Like 1;
Chain: A
Fragment: Unp Residues 391-593,Unp Residues 391-593
Synonym: 107 Kda Retinoblastoma-Associated Protein,P107,Prb Retinoblastoma-Associated Protein,P107,Prb1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rbl1
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Hpv E7 Peptide
Chain: B
Engineered: Yes

Organism_scientific: Human Papillomavirus
Organism_taxid: 10566
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
symmetry Space Group: C 1 2 1
R_factor 0.184 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
99.690 76.550 74.680 90.00 120.32 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand SO4 enzyme

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] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (4yoz.pdb1.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 4YOZ
  • CSU: Contacts of Structural Units for 4YOZ
  • Structure Factors (251 Kb)
  • Retrieve 4YOZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YOZ from S2C, [Save to disk]
  • Re-refined 4yoz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YOZ 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 4YOZ
  • 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 4yoz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yoz_A] [4yoz] [4yoz_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YOZ: [CYCLIN] [RB_A ] by SMART
  • Other resources with information on 4YOZ
  • Community annotation for 4YOZ at PDBWiki (http://pdbwiki.org)

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