OCA Atlas for 1AQD
1AQD Complex (Mhc Protein Antigen) date Jul 28, 1997
title Hla-Dr1 (Dra, Drb1 0101) Human Class II Histocompatibility Protein (Extracellular Domain) Complexed With Endogenous Peptide
authors V.L.Murthy, L.J.Stern
compound source
Molecule: Hla-Dr1 Class II Histocompatibility Protein
Chain: A, B, D, E, G, H, J, K
Fragment: Secreted Extracellular Domains
Synonym: Dra, Drb1 01010
Engineered: Yes
Biological_unit: Heterodimer
 Organism_scientific: Homo Sapiens
Organism_common: Human
Tissue: Lymphoid
Cellular_location: Plasma Membrane
Gene: Dra0101, Drb10101
Expression_system: Spodoptera Frugiperda Insect Cells
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pvl1392-Based

Molecule: Hla-A2
Chain: C, F, I, L
Fragment: Antigenic Peptide
Engineered: Yes
Other_details: Hla-Dr1 Is A Class II Mhc Protein, Hla-A2 Is A Class I Histocompatibility Antigen
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Cell: Lymphoid
Cellular_location: Plasma Membrane
symmetry Space Group: C 1 2 1
R_factor 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.514 134.320 131.232 90.00 104.82 90.00
method X-Ray Diffractionresolution 2.45 Å
related structures by homologous chain: 1D5X, 1D6E, 1SEB
similarity Belongs to the MHC_II_alpha family.
subunit Dimer of alpha chain and a beta chain (beta-2- microglobulin).
polymorphism The following alleles of a-2 are known a*0202, a*0203, a*0204, a*0205, a*0206 (a2.4a), a*0207, a*0208, a*0209, a*0210, a*0211 (a2.5), a*0212, a*0213 (a*02slu), a*0216, a*0217, a*0218 (a2k), a*0219, a*0220 and a*0221. The sequence shown is that of a*0201.
genes HLA-A, HLA-DRA, HLAA (H. sapiens)
function Involved in the presentation of foreign antigens to the immune system.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (287 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1AQD
  • Likely Quarternary Molecular Structure file(s) for 1AQD
  • Structure Factors (r1aqdsf.ent.Z) 720 Kb
  • Retrieve 1AQD in mmCIF format [Save to disk]
    • View 1AQD 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 1AQD
  • 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 1AQD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1aqda2, region A:3-81 [rasmolscript] [script source]
        - Domain d1aqda1, region A:82-181 [rasmolscript] [script source]
        - Domain d1aqdb2, region B:4-92 [rasmolscript] [script source]
        - Domain d1aqdb1, region B:93-190 [rasmolscript] [script source]
        - Domain d1aqdd2, region D:3-81 [rasmolscript] [script source]
        - Domain d1aqdd1, region D:82-179 [rasmolscript] [script source]
        - Domain d1aqde2, region E:4-92 [rasmolscript] [script source]
        - Domain d1aqde1, region E:93-190 [rasmolscript] [script source]
        - Domain d1aqdg2, region G:3-81 [rasmolscript] [script source]
        - Domain d1aqdg1, region G:82-179 [rasmolscript] [script source]
        - Domain d1aqdh2, region H:4-92 [rasmolscript] [script source]
        - Domain d1aqdh1, region H:93-190 [rasmolscript] [script source]
        - Domain d1aqdj2, region J:3-81 [rasmolscript] [script source]
        - Domain d1aqdj1, region J:82-179 [rasmolscript] [script source]
        - Domain d1aqdk2, region K:4-92 [rasmolscript] [script source]
        - Domain d1aqdk1, region K:93-191 [rasmolscript] [script source]
  • Fold representative 1aqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Domain Definition for 1aqd 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: [1aqd_A] [1aqd_B] [1aqd_C] [1aqd_D] [1aqd_E] [1aqd_F] [1aqd_G] [1aqd_H] [1aqd_I] [1aqd_J] [1aqd_K] [1aqd_L]
  • SWISS-PROT database: [1A02_HUMAN] [HA2R_HUMAN] [HB2F_HUMAN]
  • Domain organization of [1A02_HUMAN] [HA2R_HUMAN] [HB2F_HUMAN] by SWISSPFAM
  • Domain found in 1AQD: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_II_alpha (PF00993) of Pfam.
  • Alignments of the sequence of 1AQD with the sequences similar proteins can be viewed for classification [1A02_HUMAN] [HA2R_HUMAN] [HB2F_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 [1A02_HUMAN] [HA2R_HUMAN] [HB2F_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1AQD
  • InterPro: IPR003006 , IPR001039 , IPR003597 , IPR000353 , IPR001003
  • 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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