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
crystal cell	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 Diffraction	resolution	2.40 Å
ligand	NAG, SO4	enzyme
related structures	by homologous chain: 1I3R, 1J8H, 1JK8
Gene Ontology	Chain Function Process Component A, C D, B
Primary reference	Structural 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

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 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] 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)

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