OCA Atlas for 1JPG
1JPG Immune System date Aug 02, 2001
title Crystal Structure Of The Lcmv Peptidic Epitope Np396 In Complex With The Murine Class I Mhc Molecule H-2db
authors C.Ciatto, A.C.Tissot, M.Tschopp, G.Capitani, F.Pecorari, A.Pluckthun, M.G.Grutter
compound source
Molecule: H-2 Class I Histocompatibility Antigen, D-B Alpha Chain;
Chain: A
Fragment: Extracellular Domains
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Expression_system: Escherichia Coli
Expression_system_common: Bacteria

Molecule: Beta-2-Microglobulin
Chain: B
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Expression_system: Escherichia Coli
Expression_system_common: Bacteria

Molecule: Lcmv Peptidic Epitope Np396
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Solid-Phase Peptide Synthesis
symmetry Space Group: C 1 2 1
R_factor 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.122 109.952 57.744 90.00 122.88 90.00
method X-Ray Diffractionresolution 2.2 Å
similarity Contains 1 immunoglobulin-like domain.[ig]
polymorphism The sequence shown is that of allele a. The following alleles of b2m are known w3, w4, and w5 (c).
subcellular loc. Secreted.
gene B2M (M. musculus)
function Beta-2-microglobulin is the beta-chain of major histocompatibility complex class i molecules.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1JPG
  • Likely Quarternary Molecular Structure file(s) for 1JPG
  • Structure Factors (r1jpgsf.ent.Z) 241 Kb
  • Retrieve 1JPG in mmCIF format [Save to disk]
    • View 1JPG in 3D
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • FirstGlance in Chemscape Chime (Install Chime freeware) This is good for easiest viewing of basic structure.
  • RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1JPG
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Fold representative 1jpg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily: CATH
  • Summaries and structural analyses of PDB data files: PDBSum
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1jpg_A] [1jpg_B] [1jpg_C]
  • SWISS-PROT database: [B2MG_MOUSE]
  • Domain organization of [B2MG_MOUSE] by SWISSPFAM
  • Domain found in 1JPG: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family ig (PF00047) of Pfam.
  • Alignments of the sequence of 1JPG with the sequences similar proteins can be viewed for classification [B2MG_MOUSE] 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 [B2MG_MOUSE] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1JPG
  • InterPro: IPR003006 , IPR003597
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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