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
  • Alignments of the sequence of 3QXD with the sequences similar proteins can be viewed for 3QXD's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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