3VXP Immune System date Sep 20, 2012
title Hla-A24 In Complex With Hiv-1 Nef134-10(6l)
authors A.Shimizu, S.Fukai, A.Yamagata, A.Iwamoto
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-24 Alph
Chain: A, D
Fragment: Unp Residues 25-298
Synonym: Aw-24, Hla Class I Histocompatibility Antigen, A-9 Chain, Mhc Class I Antigen A24;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d(+)

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
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a(+)

Molecule: 10-Mer Peptide From Protein Nef
Chain: C, F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.731 88.741 155.829 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
Gene
Ontology
ChainFunctionProcessComponent
E, B
  • cellular response to iron io...

    • Primary referenceStructure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection., Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A, Sci Rep. 2013 Nov 6;3:3097. doi: 10.1038/srep03097. PMID:24192765
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (3vxp.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3vxp.pdb2.gz) 67 Kb
  • CSU: Contacts of Structural Units for 3VXP
  • Structure Factors (512 Kb)
  • Retrieve 3VXP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VXP from S2C, [Save to disk]
  • Re-refined 3vxp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VXP 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 3VXP
  • 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 3VXP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vxp_F] [3vxp] [3vxp_A] [3vxp_C] [3vxp_D] [3vxp_B] [3vxp_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VXP: [IGc1 ] by SMART
    • Other resources with information on 3VXP
  • Community annotation for 3VXP at PDBWiki (http://pdbwiki.org)

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