1P4L Immune System date Apr 23, 2003
title Crystal Structure Of Nk Receptor Ly49c Mutant With Its Mhc C Ligand H-2kb
authors J.Dam, R.Guan, K.Natarajan, N.Dimasi, R.A.Mariuzza
compound source
Molecule: Mhc Class I H-2kb Heavy Chain
Chain: A
Fragment: Extracellular Alpha-1, Alpha-2, Alpha-3
Synonym: H-2 Class I Histocompatibility Antigen, K-B Alpha 2kb;
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: H2-K
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Beta-2-Microglobulin
Chain: B
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: B2m
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ovalbumin Peptide
Chain: P
Engineered: Yes
Other_details: Antigenic Peptide
Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Of The Peptide Is Naturally Found In Gallus Gallus (Chicken

Molecule: Ly49-C
Chain: D
Fragment: C-Type Lectin-Like Domain
Synonym: Killer Cell Lectin-Like Receptor 3, T-Cell Surface Glycoprotein Ly-49c, Lymphocyte Antigen 49c, 5e6;
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Klra3 Or Ly49c Or Ly-49c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.269 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.010 152.010 64.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
related structures by homologous chain: 1B0R, 1N59
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceVariable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b)., Dam J, Guan R, Natarajan K, Dimasi N, Chlewicki LK, Kranz DM, Schuck P, Margulies DH, Mariuzza RA, Nat Immunol 2003 Dec;4(12):1213-22. PMID:14595439
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (1p4l.pdb1.gz) 154 Kb
  • CSU: Contacts of Structural Units for 1P4L
  • Likely Quarternary Molecular Structure file(s) for 1P4L
  • Structure Factors (235 Kb)
  • Retrieve 1P4L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1P4L from S2C, [Save to disk]
  • Re-refined 1p4l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1P4L 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 1P4L
  • 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 1P4L, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p4la1, region A:182-274 [Jmol] [rasmolscript] [script source]
        - Domain d1p4la2, region A:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1p4lb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1p4ld_, region D [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: [1p4l_B] [1p4l_P] [1p4l_D] [1p4l_A] [1p4l]
  • SWISS-PROT database: [P01887] [P01901] [Q64329] [P01012]
  • Domain organization of [B2MG_MOUSE] [HA1B_MOUSE] [KLRA3_MOUSE] [OVAL_CHICK] by SWISSPFAM
  • Domains found in 1P4L: [CLECT] [IGc1 ] by SMART
    • Other resources with information on 1P4L
  • Community annotation for 1P4L 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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