OCA Atlas for 1AKJ
1AKJ Complex (Mhc I Peptide Cd8) date May 21, 1997
title Complex Of The Human Mhc Class I Glycoprotein Hla-A2 And The T Cell Coreceptor Cd8
authors G.F.Gao, J.Tormo, U.C.Gerth, J.R.Wyer, A.J.Mcmichael, D.I.Stuart, J.I.Bell, E.Y.Jones, B.K.Jakobsen
compound source
Molecule: Mhc Class I Histocompatibility Antigen
Chain: A, B
Fragment: Extracellular Domain
Synonym: Hla-A2, Hla-A0201
Engineered: Yes
Biological_unit: Dimer Of Alpha Chain (Chain A) And A Beta Chain Of Beta-2-Microglobulin (Chain B);
 Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 (De3) Plyss
Expression_system_vector: Pet23d
Expression_system_plasmid: Bj075

Molecule: Hiv Reverse Transcriptase Epitope
Chain: C
Fragment: Peptide, Residues 309 - 317
Engineered: Yes
Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus

Molecule: T-Cell Coreceptor Cd8
Chain: D, E
Fragment: Extracellular Igsf Domain, Residues 1 - 120, Alpha Chain;
Engineered: Yes
Biological_unit: Alpha-Alpha Homodimer
Organism_scientific: Homo Sapiens
Organism_common: Human
Expression_system: Escherichia Coli
Expression_system_strain: Bl21 (De3) Plyss
Expression_system_vector: Pgmt7
Expression_system_plasmid: Bj112
symmetry Space Group: P 21 21 21
R_factor 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.900 89.600 116.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
related structures by homologous chain: 1HHG, 1QRN
similarity Belongs to the immunoglobulin superfamily. Contains 1 immunoglobulin-like v-type domain.[ig]
subunit Can also forms homodimers. In general heterodimer of an alpha and a beta chain linked by two disulfide bonds.
post-translat. modifications All of the five most carboxyl-terminal cysteines are used to form inter-chain disulfide bonds in dimers and higher multimers, while the four amino-terminal cysteines are not (by similarity).
subcellular loc. Type i membrane protein.
genes CD8A, MAL (H. sapiens)
function Cd8 is thought to play a role in the process of t-cell mediated killing. Identifies cytotoxic/suppressor t-cells that interact with mhc class i bearing targets. Cd8 alpha chains binds to class i mhc molecules alpha-3 domains.
disease Megakaryoblastic leukemia,acute
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1AKJ
  • Likely Quarternary Molecular Structure file(s) for 1AKJ
  • Structure Factors (r1akjsf.ent.Z) 165 Kb
  • Retrieve 1AKJ in mmCIF format [Save to disk]
    • View 1AKJ 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 1AKJ
  • 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.
  • GRASS (Graphical Representation and Analysis of Structure Server)
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Genome occurence of 1AKJ's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1akja2, region A:1-181 [rasmolscript] [script source]
        - Domain d1akja1, region A:182-276 [rasmolscript] [script source]
        - Domain d1akjb1, region B: [rasmolscript] [script source]
        - Domain d1akjd_, region D: [rasmolscript] [script source]
        - Domain d1akje_, region E: [rasmolscript] [script source]
  • Fold representative 1akj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Domain Definition for 1akj from 3Dee ( The Database of Protein Domain Definitions )
  • 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: [1akj_A] [1akj_B] [1akj_C] [1akj_D] [1akj_E]
  • SWISS-PROT database: [CD8A_HUMAN]
  • Domain organization of [CD8A_HUMAN] by SWISSPFAM
  • Domains found in 1AKJ: [IGc1] [IGv ] by SMART
  • Conserved protein region description, domain view and alignment from family ig (PF00047) of Pfam.
  • Alignments of the sequence of 1AKJ with the sequences similar proteins can be viewed for classification [CD8A_HUMAN] 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 [CD8A_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1AKJ
  • InterPro: IPR003006 , IPR003596
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1AKJ from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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