1PYW Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus hemagglutinin, FVKQNA(MAA)AL, in complex with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2) date
authors Zavala-Ruiz, Z., Sundberg, E.J., Stone, J.D., DeOliveira, D.B., Chan, I.C., Svendsen, J., Mariuzza, R.A., Stern, L.J.
compound source
symmetry
R_factor
R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand ACE, MAA enzyme
related structures by homologous chain: 1D5M, 1I4Q, 1I4R, 1MUJ, 1SJH
Gene
Ontology
ChainFunctionProcessComponent
A


B


D
  • toxin activity


  • Primary referenceExploration of the P6/P7 region of the peptide-binding site of the human class II major histocompatability complex protein HLA-DR1., Zavala-Ruiz Z, Sundberg EJ, Stone JD, DeOliveira DB, Chan IC, Svendsen J, Mariuzza RA, Stern LJ, J Biol Chem 2003 Nov 7;278(45):44904-12. Epub 2003 Sep 1. PMID:12952957
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (1pyw.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 1PYW
  • CSU: Contacts of Structural Units for 1PYW
  • Likely Quarternary Molecular Structure file(s) for 1PYW
  • Structure Factors (664 Kb)
  • Retrieve 1PYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PYW from S2C, [Save to disk]
  • Re-refined 1pyw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PYW 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 1PYW
  • 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
  • 3D motif for 1PYW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pywa2, region A:4-81 [Jmol] [rasmolscript] [script source]
        - Domain d1pywa1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1pywb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1pywb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1pywd1, region D:1-121 [Jmol] [rasmolscript] [script source]
        - Domain d1pywd2, region D:122-239 [Jmol] [rasmolscript] [script source]
  • 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: [1pyw] [1pyw_C] [1pyw_A] [1pyw_D] [1pyw_B]
  • SWISS-PROT database: [P04229] [P01903]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] by SWISSPFAM
  • Domains found in 1PYW: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1PYW
  • Community annotation for 1PYW 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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