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
crystal
cell
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
  • Alignments of the sequence of 3L6F with the sequences similar proteins can be viewed for 3L6F'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 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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