3QFD Immune System date Jan 21, 2011
title Human Class I Mhc Hla-A2 In Complex With Mart-1(27-35) Nonam Peptide
authors O.Y.Borbulevych, B.M.Baker
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha
Chain: A, D
Synonym: Mhc Class I Antigen A2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A, Hlaa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phn1

Molecule: Beta-2-Microglobulin
Chain: B, E
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phn1

Molecule: Mart-1(27-35) Peptide
Chain: C, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.254 84.118 83.964 90.00 90.05 90.00
method X-Ray Diffractionresolution 1.68 Å
ligand GOL, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
E, B
  • cellular response to iron io...

  • Primary referenceLoss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design., Insaidoo F, Borbulevych OY, Hossain M, Santhanagopolan SM, Baxter TK, Baker BM, J Biol Chem. 2011 Sep 21. PMID:21937447
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (288 Kb) [Save to disk]
  • Biological Unit Coordinates (3qfd.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (3qfd.pdb2.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 3QFD
  • CSU: Contacts of Structural Units for 3QFD
  • Structure Factors (1346 Kb)
  • Retrieve 3QFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QFD from S2C, [Save to disk]
  • Re-refined 3qfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QFD 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 3QFD
  • 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
  • 3D motif for 3QFD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qfd_A] [3qfd_B] [3qfd_D] [3qfd_F] [3qfd_E] [3qfd_C] [3qfd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3QFD: [IGc1 ] by SMART
  • Other resources with information on 3QFD
  • Community annotation for 3QFD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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