4O2C Immune System date Dec 17, 2013
title An Nt-Acetylated Peptide Complexed With Hla-B3901
authors M.Sun, J.Liu, J.Qi, B.Tefsen, Y.Shi, J.Yan, G.F.Gao
compound source
Molecule: Hla Class I Histocompatibility Antigen, B-39 Alph
Chain: A
Fragment: Unp Residues 25-298
Synonym: Mhc Class I Antigen B39
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-B, Hlab
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Beta-2-Microglobulin
Chain: B
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_vector_type: Plasmid

Molecule: Peptide From Atp-Dependent Rna Helicase Ddx3x
Chain: C
Synonym: Dead Box Protein 3, X-Chromosomal, Dead Box, X Iso Helicase-Like Protein 2, Hlp2;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.174 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.845 81.459 110.958 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand ACE enzyme
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referenceNalpha-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted nalpha-acetylpeptide presentation., Sun M, Liu J, Qi J, Tefsen B, Shi Y, Yan J, Gao GF, J Immunol. 2014 Jun 15;192(12):5509-19. doi: 10.4049/jimmunol.1400199. Epub 2014 , May 14. PMID:24829406
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (4o2c.pdb1.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 4O2C
  • CSU: Contacts of Structural Units for 4O2C
  • Structure Factors (702 Kb)
  • Retrieve 4O2C in mmCIF format [Save to disk]
  • Re-refined 4o2c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4O2C in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4O2C
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  • 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 4O2C, from MSDmotif at EBI
  • Fold representative 4o2c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4o2c] [4o2c_C] [4o2c_B] [4o2c_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4O2C: [IGc1 ] by SMART
  • Other resources with information on 4O2C
  • Community annotation for 4O2C at PDBWiki (http://pdbwiki.org)

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