1D6E Immune System Peptide Inhibitor date Oct 13, 1999
title Crystal Structure Of Hla-Dr4 Complex With Peptidomimetic And
authors A.Swain, R.Crowther, U.Kammlott
compound source
Molecule: Hla Class II Histocompatibility Antigen
Chain: A
Fragment: Dr Alpha Chain, Extracellular Domain
Synonym: Hla-Dr4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227

Molecule: Hla Class II Histocompatibility Antigen
Chain: B
Fragment: Dr-4 Beta Chain, Extracellular Domain
Synonym: Hla-Dr4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227

Molecule: Enterotoxin Type B
Chain: C
Synonym: Seb, Superantigen

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280

Molecule: Peptidomimetic Inhibitor
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.827 102.335 102.638 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand ACE, ALC, BUG, MPQ, NH2, TBG enzyme
related structures by homologous chain: 1AQD, 1D5X, 1SJE
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


Primary referencePeptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures., Bolin DR, Swain AL, Sarabu R, Berthel SJ, Gillespie P, Huby NJ, Makofske R, Orzechowski L, Perrotta A, Toth K, Cooper JP, Jiang N, Falcioni F, Campbell R, Cox D, Gaizband D, Belunis CJ, Vidovic D, Ito K, Crowther R, Kammlott U, Zhang X, Palermo R, Weber D, Guenot J, Nagy Z, Olson GL, J Med Chem 2000 Jun 1;43(11):2135-48. PMID:10841792
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (1d6e.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 1D6E
  • CSU: Contacts of Structural Units for 1D6E
  • Likely Quarternary Molecular Structure file(s) for 1D6E
  • Structure Factors (297 Kb)
  • Retrieve 1D6E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D6E from S2C, [Save to disk]
  • Re-refined 1d6e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D6E 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 1D6E
  • 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 1D6E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d6ea2, region A:4-81 [Jmol] [rasmolscript] [script source]
        - Domain d1d6ea1, region A:82-180 [Jmol] [rasmolscript] [script source]
        - Domain d1d6eb2, region B:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1d6eb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1d6ec2, region C:122-237 [Jmol] [rasmolscript] [script source]
        - Domain d1d6ec1, region C:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d6e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d6e] [1d6e_A] [1d6e_D] [1d6e_B] [1d6e_C]
  • SWISS-PROT database: [P13760] [P01903] [P01552]
  • Domain organization of [2B14_HUMAN] [DRA_HUMAN] [ETXB_STAAU] by SWISSPFAM
  • Domains found in 1D6E: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1D6E with the sequences similar proteins can be viewed for 1D6E's classification [2B14_HUMAN] [DRA_HUMAN] [ETXB_STAAU] 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 [2B14_HUMAN] [DRA_HUMAN] [ETXB_STAAU] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1D6E
  • Community annotation for 1D6E 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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