3S5L Immune System date May 23, 2011
title Crystal Structure Of Cd4 Mutant Bound To Hla-Dr1
authors Y.Li
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A, D
Fragment: Mhc Class II A Chain
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: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-26b

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 B
Chain: B, E
Fragment: Mhc Class II B Chain
Synonym: Mhc Class II 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
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-26b

Molecule: Ha Peptide
Chain: C, F
Fragment: Ha Peptide
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Chemical Synthesis

Molecule: T-Cell Surface Glycoprotein Cd4
Chain: G, H
Fragment: Cd4
Synonym: T-Cell Surface Antigen T4leu-3
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd4
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacgp67-B
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.200 119.700 137.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand GOL enzyme
Primary referenceAffinity maturation of human CD4 by yeast surface display and crystal structure of a CD4-HLA-DR1 complex., Wang XX, Li Y, Yin Y, Mo M, Wang Q, Gao W, Wang L, Mariuzza RA, Proc Natl Acad Sci U S A. 2011 Sep 7. PMID:21900604
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (193 Kb) [Save to disk]
  • Biological Unit Coordinates (3s5l.pdb1.gz) 96 Kb
  • Biological Unit Coordinates (3s5l.pdb2.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 3S5L
  • CSU: Contacts of Structural Units for 3S5L
  • Structure Factors (772 Kb)
  • Retrieve 3S5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3S5L from S2C, [Save to disk]
  • Re-refined 3s5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3S5L 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 3S5L
  • 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 3S5L, from MSDmotif at EBI
  • Fold representative 3s5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3s5l_F] [3s5l_H] [3s5l_D] [3s5l_G] [3s5l_C] [3s5l_E] [3s5l_B] [3s5l_A] [3s5l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3S5L: [IG] [IGc1] [IGv] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 3S5L
  • Community annotation for 3S5L at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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