1D5Z Immune System Peptide Inhibitor date Oct 12, 1999
title X-Ray Crystal Structure Of Hla-Dr4 Complexed With Peptidomim Seb
authors A.Swain, R.Crowther, U.Kammlott
compound source
Molecule: Protein (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: Protein (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: Protein (Enterotoxin Type B)
Chain: C
Synonym: Seb, Superantigen

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280

Molecule: Protein (Peptidomimetic Inhibitor)
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.343 100.168 100.175 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ACE, ALC, CLE, NH2, ODA enzyme
related structures by homologous chain: 1D5M, 1GOZ, 1KLU
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] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5z.pdb1.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 1D5Z
  • CSU: Contacts of Structural Units for 1D5Z
  • Likely Quarternary Molecular Structure file(s) for 1D5Z
  • Structure Factors (493 Kb)
  • Retrieve 1D5Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5Z from S2C, [Save to disk]
  • Re-refined 1d5z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D5Z 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 1D5Z
  • 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 1D5Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5za2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1d5za1, region A:82-180 [Jmol] [rasmolscript] [script source]
        - Domain d1d5zb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1d5zb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1d5zc2, region C:122-237 [Jmol] [rasmolscript] [script source]
        - Domain d1d5zc1, region C:2-121 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5z 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: [1d5z_B] [1d5z_C] [1d5z] [1d5z_D] [1d5z_A]
  • SWISS-PROT database: [P13760] [P01903] [P01552]
  • Domain organization of [2B14_HUMAN] [DRA_HUMAN] [ETXB_STAAU] by SWISSPFAM
  • Domains found in 1D5Z: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1D5Z with the sequences similar proteins can be viewed for 1D5Z'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 1D5Z
  • Community annotation for 1D5Z at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science