4IRV Protein Binding date Jan 15, 2013
title Structure Of The Helicobacter Pylori Caga Oncogene Bound To Tumor Suppressor Apoptosis-Stimulating Protein Of P53-2
authors C.E.Stebbins, D.Nesic
compound source
Molecule: Cytotoxicity-Associated Immunodominant Antigen
Chain: A, B, C, D
Synonym: 120 Kda Protein, Cag Pathogenicity Island Protein
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Organism_taxid: 85962
Strain: Atcc 700392 26695
Gene: Caga, Cag26, Cai, Hp_0547
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Apoptosis-Stimulating Of P53 Protein 2
Chain: E, F, G, H
Synonym: Bcl2-Binding Protein, Bbp, Renal Carcinoma Antigen 51, Tumor Suppressor P53-Binding Protein 2, 53bp2, P53-Bind Protein 2, P53bp2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aspp2, Bbp, Tp53bp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
118.641 120.239 100.659 90.00 115.64 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand MSE enzyme
Gene HP
A, D, C, B

Primary referenceStructure of the Helicobacter pylori CagA oncoprotein bound to the human tumor suppressor ASPP2., Nesic D, Buti L, Lu X, Stebbins CE, Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1562-7. doi:, 10.1073/pnas.1320631111. Epub 2014 Jan 13. PMID:24474782
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (4irv.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (4irv.pdb2.gz) 40 Kb
  • Biological Unit Coordinates (4irv.pdb3.gz) 39 Kb
  • Biological Unit Coordinates (4irv.pdb4.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 4IRV
  • CSU: Contacts of Structural Units for 4IRV
  • Structure Factors (912 Kb)
  • Retrieve 4IRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IRV from S2C, [Save to disk]
  • Re-refined 4irv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IRV 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 4IRV
  • 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 4IRV, from MSDmotif at EBI
  • Fold representative 4irv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4irv_B] [4irv_H] [4irv_E] [4irv] [4irv_F] [4irv_C] [4irv_D] [4irv_G] [4irv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4IRV
  • Community annotation for 4IRV 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