5D6D Immune System date Aug 12, 2015
title Crystal Structure Of Gasdalie Igg1 Fc In Complex With Fcgrii
authors A.A.Ahmed, P.J.Bjorkman
compound source
Molecule: Ig Gamma-1 Chain C Region
Chain: A, B
Fragment: Unp Residues 109-329
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ighg1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606

Molecule: Low Affinity Immunoglobulin Gamma Fc Region Recep
Chain: C
Fragment: Unp Residues 14-205
Synonym: Cd16a Antigen,Fc-Gamma Riii-Alpha,Fcriiia,Fcr-10,I Receptor III-2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fcgr3a, Cd16a, Fcg3, Fcgr3, Igfr3
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.271 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.380 94.500 108.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.13 Å
ligand BMA, FUC, FUL, GAL, MAN, NAG enzyme
Primary referenceStructural characterization of GASDALIE Fc bound to the activating Fc receptor FcgammaRIIIa., Ahmed AA, Keremane SR, Vielmetter J, Bjorkman PJ, J Struct Biol. 2016 Apr;194(1):78-89. doi: 10.1016/j.jsb.2016.02.001. Epub 2016, Feb 2. PMID:26850169
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (5d6d.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 5D6D
  • CSU: Contacts of Structural Units for 5D6D
  • Structure Factors (741 Kb)
  • Retrieve 5D6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D6D from S2C, [Save to disk]
  • Re-refined 5d6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D6D 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 5D6D
  • 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: [5d6d] [5d6d_C] [5d6d_A] [5d6d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5D6D: [IG] [IG_like] [IGc1 ] by SMART
  • Other resources with information on 5D6D
  • Community annotation for 5D6D at PDBWiki (http://pdbwiki.org)

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