1D5X Immune System Peptide Inhibitor date Oct 12, 1999
title X-Ray Crystal Structure Of Hla-Dr4 Complexed With Dipeptide And Seb
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: Dipeptide Mimetic Inhibitor
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.237 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.838 104.252 107.818 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand ACE, ALC, HAQ, MAA, SEL enzyme
related structures by homologous chain: 1AQD, 1D6E, 1T5X
Gene
Ontology
ChainFunctionProcessComponent
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 (1d5x.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 1D5X
  • CSU: Contacts of Structural Units for 1D5X
  • Likely Quarternary Molecular Structure file(s) for 1D5X
  • Structure Factors (357 Kb)
  • Retrieve 1D5X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5X from S2C, [Save to disk]
  • Re-refined 1d5x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D5X 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 1D5X
  • 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 1D5X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5xa2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1d5xa1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1d5xb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1d5xb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1d5xc2, region C:122-238 [Jmol] [rasmolscript] [script source]
        - Domain d1d5xc1, region C:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5x 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: [1d5x_A] [1d5x_B] [1d5x] [1d5x_D] [1d5x_C]
  • SWISS-PROT database: [P13760] [P01903] [P01552]
  • Domain organization of [2B14_HUMAN] [DRA_HUMAN] [ETXB_STAAU] by SWISSPFAM
  • Domains found in 1D5X: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1D5X with the sequences similar proteins can be viewed for 1D5X'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 1D5X
  • Community annotation for 1D5X 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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