4KJY Immune System date May 04, 2013
title Complex Of High-Affinity Sirp Alpha Variant Fd6 With Cd47
authors A.M.Ring, E.Ozkan, C.C.M.Ho, K.C.Garcia
compound source
Molecule: Leukocyte Surface Antigen Cd47
Chain: A, C
Synonym: Antigenic Surface Determinant Protein Oa3, Integri Associated Protein, Iap, Protein Mer6;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd47, Mer6
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacgp67a

Molecule: High-Affinity Sirpa Variant Fd6
Chain: B, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-P2x
symmetry Space Group: P 65 2 2
R_factor 0.219 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
71.340 71.340 399.180 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.93 Å
ligand NAG, PCA, SO4 enzyme
Primary referenceEngineered SIRPalpha variants as immunotherapeutic adjuvants to anticancer antibodies., Weiskopf K, Ring AM, Ho CC, Volkmer JP, Levin AM, Volkmer AK, Ozkan E, Fernhoff NB, van de Rijn M, Weissman IL, Garcia KC, Science. 2013 Jul 5;341(6141):88-91. doi: 10.1126/science.1238856. Epub 2013 May , 30. PMID:23722425
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (4kjy.pdb1.gz) 81 Kb
  • Biological Unit Coordinates (4kjy.pdb2.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 4KJY
  • CSU: Contacts of Structural Units for 4KJY
  • Structure Factors (234 Kb)
  • Retrieve 4KJY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KJY from S2C, [Save to disk]
  • Re-refined 4kjy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KJY 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 4KJY
  • 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 4KJY, from MSDmotif at EBI
  • Fold representative 4kjy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kjy_C] [4kjy_D] [4kjy_B] [4kjy] [4kjy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KJY: [IG] [IG_like ] by SMART
  • Other resources with information on 4KJY
  • Community annotation for 4KJY at PDBWiki (http://pdbwiki.org)

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