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
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


H, G


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
  • Alignments of the sequence of 3S5L with the sequences similar proteins can be viewed for 3S5L'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 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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