3QXD Immune System date Mar 01, 2011
title F54c Hla-Dr1 Bound With Clip Peptide
authors C.A.Painter, L.J.Stern
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A, D
Fragment: Unp Residues 26-207
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dr1, Hla-Dra, Hla-Dra1
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B
Chain: B, E
Fragment: Unp Residues 30-219
Synonym: Mhc Class II Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dr1, Hla-Drb1
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid

Molecule: Hla Class II Histocompatibility Antigen Gamma Cha Peptide;
Chain: F, C
Fragment: Clip Region
Synonym: Hla-Dr Antigens-Associated Invariant Chain, Ia Ant Associated Invariant Chain, II, P33;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Chemically Synthesized Sequence Occurs In Human
symmetry Space Group: P 21 21 21
R_factor 0.189 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.001 94.870 154.090 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
Primary referenceConformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange., Painter CA, Negroni MP, Kellersberger KA, Zavala-Ruiz Z, Evans JE, Stern LJ, Proc Natl Acad Sci U S A. 2011 Nov 14. PMID:22084083
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (264 Kb) [Save to disk]
  • Biological Unit Coordinates (3qxd.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (3qxd.pdb2.gz) 130 Kb
  • CSU: Contacts of Structural Units for 3QXD
  • Structure Factors (1252 Kb)
  • Retrieve 3QXD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QXD from S2C, [Save to disk]
  • Re-refined 3qxd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QXD 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 3QXD
  • Cartoon representation from PDB Cartoon
  • 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 3QXD, from MSDmotif at EBI
  • Fold representative 3qxd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qxd] [3qxd_D] [3qxd_B] [3qxd_E] [3qxd_A] [3qxd_C] [3qxd_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3QXD: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 3QXD
  • Community annotation for 3QXD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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