5TZT Immune System date Nov 22, 2016
title Crystal Structure Of Human Cd47 Ecd Bound To Fab Of C47b161
authors R.M.F.Cardoso
compound source
Molecule: Light Chain Of Fab C47b161
Chain: B, L
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293

Molecule: Heavy Chain Of Fab C47b161
Chain: A, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293

Molecule: Leukocyte Surface Antigen Cd47
Chain: C, D
Fragment: Extracellular Domain, Unp Residues 19-141
Synonym: Antigenic Surface Determinant Protein Oa3,Integrin Associated Protein,Iap,Protein Mer6;
Engineered: Yes
Mutation: Yes
Other_details: Residue 1 Is A Gln That Cyclizes As Pyroglut (Pca)

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd47, Mer6
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
symmetry Space Group: P 1 21 1
R_factor 0.257 R_Free 0.328
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.569 60.974 124.133 90.00 90.05 90.00
method X-Ray Diffractionresolution 2.89 Å
ligand GOL, NAG, PCA enzyme
Primary referenceAnti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies., Pietsch EC, Dong J, Cardoso R, Zhang X, Chin D, Hawkins R, Dinh T, Zhou M, Strake B, Feng PH, Rocca M, Santos CD, Shan X, Danet-Desnoyers G, Shi F, Kaiser E, Millar HJ, Fenton S, Swanson R, Nemeth JA, Attar RM, Blood Cancer J. 2017 Feb 24;7(2):e536. doi: 10.1038/bcj.2017.7. PMID:28234345
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (350 Kb) [Save to disk]
  • Biological Unit Coordinates (5tzt.pdb1.gz) 171 Kb
  • Biological Unit Coordinates (5tzt.pdb2.gz) 171 Kb
  • LPC: Ligand-Protein Contacts for 5TZT
  • CSU: Contacts of Structural Units for 5TZT
  • Structure Factors (637 Kb)
  • Retrieve 5TZT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TZT from S2C, [Save to disk]
  • Re-refined 5tzt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TZT 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 5TZT
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tzt_L] [5tzt_A] [5tzt_B] [5tzt_D] [5tzt] [5tzt_C] [5tzt_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TZT
  • Community annotation for 5TZT at PDBWiki (http://pdbwiki.org)

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