3L6F Immune System Peptide Binding Protein date Dec 23, 2009
title Structure Of Mhc Class II Molecule Hla-Dr1 Complexed With Phosphopeptide Mart-1
authors Y.Li, R.A.Mariuzza
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Fragment: Unp Residues 26-207
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra, Hla-Dra1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Pet-26b

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B
Chain: B
Fragment: Unp Residues 30-221
Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Melanoma Antigen Recognized By T-Cells 1
Chain: C
Fragment: Unp Residues 100-114
Synonym: Mart-1, Melan-A Protein, Antigen Sk29-Aa, Antigen
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.212 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
91.210 135.450 40.850 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand SEP enzyme


Primary referenceStructural Basis for the Presentation of Tumor-Associated MHC Class II-Restricted Phosphopeptides to CD4(+) T Cells., Li Y, Depontieu FR, Sidney J, Salay TM, Engelhard VH, Hunt DF, Sette A, Topalian SL, Mariuzza RA, J Mol Biol. 2010 Apr 24. PMID:20417641
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (3l6f.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3L6F
  • CSU: Contacts of Structural Units for 3L6F
  • Structure Factors (241 Kb)
  • Retrieve 3L6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L6F from S2C, [Save to disk]
  • Re-refined 3l6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L6F 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 3L6F
  • 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 3L6F, from MSDmotif at EBI
  • Fold representative 3l6f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l6f_C] [3l6f_A] [3l6f] [3l6f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3L6F: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 3L6F
  • Community annotation for 3L6F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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