1FYT Immune System date Oct 03, 2000
title Crystal Structure Of A Complex Of A Human Alphabeta-T Cell Influenza Ha Antigen Peptide, And Mhc Class II Molecule, Hl
authors J.Hennecke, A.Carfi, D.C.Wiley
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha
Chain: A
Fragment: Extracellular Domain
Synonym: Hla-Dr1, Dra
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, Dr-1 Bet
Chain: B
Fragment: Extracellular Domain
Synonym: Hla-Dr1, Drb1 0101
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: Hemagglutinin Ha1 Peptide Chain
Chain: C
Fragment: Antigen Peptide
Engineered: Yes

Organism_scientific: H3n2 Subtype
Organism_taxid: 119210
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: T-Cell Receptor Alpha Chain
Chain: D
Fragment: Extracellular Domain
Synonym: Tcr Ha1.7 Alpha Chain
Engineered: Yes

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

Molecule: T-Cell Receptor Beta Chain
Chain: E
Fragment: Extracellular Domain
Synonym: Tcr Ha1.7 Beta Chain
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.902 73.439 122.428 90.00 108.23 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand NAG enzyme
related structures by homologous chain: 1AO7, 1BD2, 1BX2, 1ES0, 1HXY, 1R5I
Primary referenceStructure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1., Hennecke J, Carfi A, Wiley DC, EMBO J 2000 Nov 1;19(21):5611-24. PMID:11060013
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (1fyt.pdb1.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 1FYT
  • CSU: Contacts of Structural Units for 1FYT
  • Likely Quarternary Molecular Structure file(s) for 1FYT
  • Structure Factors (417 Kb)
  • Retrieve 1FYT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1FYT from S2C, [Save to disk]
  • Re-refined 1fyt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1FYT 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 1FYT
  • 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 1FYT, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1fyta2, region A:2-81 [Jmol] [rasmolscript] [script source]
        - Domain d1fyta1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1fytb2, region B:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1fytb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1fytd1, region D:1-117 [Jmol] [rasmolscript] [script source]
        - Domain d1fytd2, region D:118-203 [Jmol] [rasmolscript] [script source]
        - Domain d1fyte2, region E:119-246 [Jmol] [rasmolscript] [script source]
        - Domain d1fyte1, region E:3-118 [Jmol] [rasmolscript] [script source]
  • Fold representative 1fyt 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: [1fyt] [1fyt_D] [1fyt_B] [1fyt_E] [1fyt_C] [1fyt_A]
  • SWISS-PROT database: [P04229] [P01903] [P03437] [P01850]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_HUMAN] by SWISSPFAM
  • Domains found in 1FYT: [IG] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1FYT with the sequences similar proteins can be viewed for 1FYT's classification [2B11_HUMAN] [DRA_HUMAN] [HEMA_I68A0] [TCB_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] [HEMA_I68A0] [TCB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1FYT
  • Community annotation for 1FYT 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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