OCA Atlas for 1BZ9
1BZ9 Murine Class I Mhc Peptide Complex date Nov 06, 1998
title Crystal Structure Of Murine Class I Mhc H2-Db Complexed With A Synthetic Peptide P1027
authors R.Zhao, D.J.Loftus, E.Appella, E.J.Collins
compound source
Molecule: Class I Histocompatibility Antigen
Chain: A
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: Mouse
Cellular_location: Cell Surface
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 Plyss
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1
Other_details: Folded With Synthetic Peptide In Vitro

Molecule: Class I Histocompatibility Antigen
Chain: B
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Cellular_location: Cell Surface
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 Plyss
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plm1
Other_details: Folded With Synthetic Peptide In Vitro

Molecule: Peptide P1027 (Fapgvfpym)
Chain: C
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic
symmetry Space Group: C 1 2 1
R_factor 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.350 109.190 57.780 90.00 122.81 90.00
method X-Ray Diffractionresolution 2.80 Å
note 1BZ9 supersedes 1A9D
related structures by homologous chain: 1CE6, 1QLF
similarity Contains 1 immunoglobulin-like domain.[MHC_I]
subunit Dimer of alpha chain and a beta chain (beta-2- microglobulin).
polymorphism The sequence shown is that of allele a. The following alleles of b2m are known w3, w4, and w5 (c).
subcellular loc. Secreted.
genes B2M, H2-D (M. musculus)
function Involved in the presentation of foreign antigens to the immune system. 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 1BZ9
  • Likely Quarternary Molecular Structure file(s) for 1BZ9
  • Structure Factors (r1bz9sf.ent.Z) 158 Kb
  • Retrieve 1BZ9 in mmCIF format [Save to disk]
    • View 1BZ9 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 1BZ9
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bz9a1, region A:182-274 [rasmolscript] [script source]
        - Domain d1bz9a2, region A:2-181 [rasmolscript] [script source]
        - Domain d1bz9b1, region B: [rasmolscript] [script source]
  • Fold representative 1bz9 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: [1bz9_A] [1bz9_B] [1bz9_C]
  • SWISS-PROT database: [HA11_MOUSE] [B2MG_MOUSE]
  • Domain organization of [HA11_MOUSE] [B2MG_MOUSE] by SWISSPFAM
  • Domain found in 1BZ9: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_I (PF00129) of Pfam.
  • Alignments of the sequence of 1BZ9 with the sequences similar proteins can be viewed for classification [HA11_MOUSE] [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 [HA11_MOUSE] [B2MG_MOUSE] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1BZ9
  • InterPro: IPR003006 , IPR001039 , 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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