1PYW Immune System Protein Binding Toxin date Jul 09, 2003
title Human Class II Mhc Protein Hla-Dr1 Bound To A Designed Pepti To Influenza Virus Hemagglutinin, Fvkqna(Maa)Al, In Complex Staphylococcal Enterotoxin C3 Variant 3b2 (Sec3-3b2)
authors Z.Zavala-Ruiz, E.J.Sundberg, J.D.Stone, D.B.Deoliveira, I.C.Chan J.Svendsen, R.A.Mariuzza, L.J.Stern
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Fragment: Extracellular Domain Of Hla-Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: T7 Polymeraselac
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Dr-1 Bet
Chain: B
Fragment: Extracellular Domain Of Hla-Drb1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: T7 Polymerase Lac
Expression_system_plasmid: Plm1

Molecule: 9-Residue Influenza Virus Hemagglutinin Related P Fvkqna(Maa)Al;
Chain: C
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Based On The Central Regio Natural Occuring Peptide Derived From The Influenza Virus Hemagglutinin. Amino Terminus Is Acetylated, Alanine At Pos Is N-Methylated, And Carboxy Terminus Is Amidated.;

Molecule: Enterotoxin Type C-3
Chain: D
Fragment: Residues 28-266
Synonym: Sec3
Engineered: Yes
Mutation: Yes

Organism_scientific: Staphylococcus Aureus Subsp. Aureus Mu
Organism_taxid: 158878
Strain: Mu50atcc 700699
Gene: Entc3 Or Sav2009 Or Sa1817
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb 2151
Expression_system_vector: Lac
symmetry Space Group: H 3
R_factor 0.209 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
172.507 172.507 121.652 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand ACE, MAA enzyme
related structures by homologous chain: 1D5M, 1I4Q, 1I4R, 1MUJ, 1SJH
Gene
Ontology
ChainFunctionProcessComponent
D


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) 111 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
  • 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 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]
  • Fold representative 1pyw 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: [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
  • Alignments of the sequence of 1PYW with the sequences similar proteins can be viewed for 1PYW's classification [2B11_HUMAN] [DRA_HUMAN] 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 [2B11_HUMAN] [DRA_HUMAN] at ProtoMap. Click on the Cluster number.
  • 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.

  • 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