1JWU Immune System date Sep 05, 2001
title Crystal Structure Of The Complex Of The Mhc Class II Molecule Hla-Dr1 (Ha Peptide 306-318) With The Superantigen Sec3 Variant 3b2
authors E.J.Sundberg, P.S.Andersen, P.M.Schlievert, K.Karjalainen, R.A.Mariuzza
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Hla Class II Histocompatibility Antigen, Dr-1 Beta Chain;
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ha Peptide
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized

Molecule: Enterotoxin Type C-3
Chain: D
Synonym: Sec3
Engineered: Yes
Mutation: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3
R_factor 0.200 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.753 171.753 120.489 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
related structures by homologous chain: 1IEA, 1SE3, 1SJH
Gene
Ontology
ChainFunctionProcessComponent
D


Primary referenceStructural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation., Sundberg EJ, Andersen PS, Schlievert PM, Karjalainen K, Mariuzza RA, Structure (Camb) 2003 Sep;11(9):1151-61. PMID:12962633
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (1jwu.pdb1.gz) 106 Kb
  • CSU: Contacts of Structural Units for 1JWU
  • Likely Quarternary Molecular Structure file(s) for 1JWU
  • Structure Factors (780 Kb)
  • Retrieve 1JWU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JWU from S2C, [Save to disk]
  • Re-refined 1jwu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JWU 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 1JWU
  • 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 1JWU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jwua2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1jwua1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1jwub2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1jwub1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1jwud1, region D:1-121 [Jmol] [rasmolscript] [script source]
        - Domain d1jwud2, region D:122-239 [Jmol] [rasmolscript] [script source]
  • Fold representative 1jwu 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: [1jwu_C] [1jwu_A] [1jwu] [1jwu_B] [1jwu_D]
  • SWISS-PROT database: [P04229] [P01903] [P0A0L5]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] by SWISSPFAM
  • Domains found in 1JWU: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1JWU with the sequences similar proteins can be viewed for 1JWU's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_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 [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1JWU
  • Community annotation for 1JWU 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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