1KTD Immune System date Jan 15, 2002
title Crystal Structure Of Class II Mhc Molecule Iek Bound To Pige Cytochrome C Peptide
authors D.H.Fremont, S.Dai, H.Chiang, F.Crawford, P.Marrack, J.Kappler
compound source
Molecule: H-2 Class II Histocompatibility Antigen, E-D Alph
Chain: A, C
Synonym: H2-Ie-Alpha
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: H2-Ea
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Fusion Protein Consisting Of Cytochrome C Peptide Rich Linker, And Mhc E-Beta-K;
Chain: B, D
Engineered: Yes
Mutation: Yes
Other_details: Fusion Protein Consists Of Pigeon Cytochrome Peptide, Residues 1-14 (Aadliaylkqasak), Glycine Rich Linke Residues 15-30 (Ggggslvgggsggggs) And Mouse Mhc E-Beta-K Ch

Organism_scientific: Columba Livia, Mus Musculus
Organism_common: Rock Dove, Mouse
Organism_taxid: 8932, 10090
Gene: Cyc, H2-Eb1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
symmetry Space Group: C 1 2 1
R_factor 0.220 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
145.520 57.300 116.570 90.00 94.23 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG, SO4 enzyme
related structures by homologous chain: 1I3R, 1J8H, 1JK8
A, C

D, B

Primary referenceStructural basis of cytochrome c presentation by IE(k)., Fremont DH, Dai S, Chiang H, Crawford F, Marrack P, Kappler J, J Exp Med 2002 Apr 15;195(8):1043-52. PMID:11956295
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (1ktd.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (1ktd.pdb2.gz) 68 Kb
  • Biological Unit Coordinates (1ktd.pdb3.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 1KTD
  • CSU: Contacts of Structural Units for 1KTD
  • Likely Quarternary Molecular Structure file(s) for 1KTD
  • Structure Factors (377 Kb)
  • Retrieve 1KTD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KTD from S2C, [Save to disk]
  • Re-refined 1ktd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KTD 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 1KTD
  • 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 1KTD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ktda2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1ktda1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdb2, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdb1, region B:121-215 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdc2, region C:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdc1, region C:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdd2, region D:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1ktdd1, region D:121-215 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ktd 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: [1ktd_A] [1ktd_D] [1ktd_B] [1ktd_C] [1ktd]
  • SWISS-PROT database: [P00021] [P01904]
  • Domain organization of [CYC_COLLI] [HA21_MOUSE] by SWISSPFAM
  • Domains found in 1KTD: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1KTD
  • Community annotation for 1KTD 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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