OCA Atlas for 1A6A
1A6A Complex (Transmembrane Glycoprotein) date Feb 22, 1998
title The Structure Of An Intermediate In Class II Mhc Maturation: Clip Bound To Hla-Dr3
authors P.Ghosh, M.Amaya, E.Mellins, D.C.Wiley
compound source
Molecule: Hla-Dr3
Chain: A, B
Biological_unit: Heterodimer
 Organism_scientific: Homo Sapiens
Organism_common: Human
Cell_line: 9.5.3
Cell: B-Lymphocyte
Cellular_location: Plasma Membrane

Molecule: Clip
Chain: C
Fragment: Clip Fragment 87 - 101 Of Invariant Chain
Organism_scientific: Homo Sapiens
Organism_common: Human
Cell_line: 9.5.3
Cell: B-Lymphocyte
Cellular_location: Plasma Membrane
symmetry Space Group: P 32 1 2
R_factor 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.450 78.450 159.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.75 Å
ligand NAGenzyme
related structures by homologous chain: 1DLH, 1SEB
similarity Contains 1 thyroglobulin type-i domain.[MHC_II_alpha]
subunit Nonamer composed of three alpha/beta/gamma heterotrimers.
subcellular loc. Type ii membrane protein (potential).
genes CD74, DHLAG, HLA-DRA (H. sapiens)
function Plays a critical role in mhc class ii antigen processing by stabilizing peptide-free class ii alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to compartments where peptide loading of class ii takes place.
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1A6A
  • CSU: Contacts of Structural Units for 1A6A
  • Likely Quarternary Molecular Structure file(s) for 1A6A
  • Structure Factors (r1a6asf.ent.Z) 156 Kb
  • Retrieve 1A6A in mmCIF format [Save to disk]
    • View 1A6A 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 1A6A
  • 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 1A6A's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1a6aa2, region A:5-81 [rasmolscript] [script source]
        - Domain d1a6aa1, region A:82-180 [rasmolscript] [script source]
        - Domain d1a6ab2, region B:5-92 [rasmolscript] [script source]
        - Domain d1a6ab1, region B:93-191 [rasmolscript] [script source]
  • Fold representative 1a6a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Domain Definition for 1a6a 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: [1a6a_A] [1a6a_B] [1a6a_C]
  • SWISS-PROT database: [HA2R_HUMAN] [HG2A_HUMAN]
  • Domain organization of [HA2R_HUMAN] [HG2A_HUMAN] by SWISSPFAM
  • Domain found in 1A6A: [IGc1 ] by SMART
  • Conserved protein region description, domain view and alignment from family MHC_II_alpha (PF00993) of Pfam.
  • Alignments of the sequence of 1A6A with the sequences similar proteins can be viewed for classification [HA2R_HUMAN] [HG2A_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 [HA2R_HUMAN] [HG2A_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1A6A
  • InterPro: IPR003006 , IPR003597 , IPR000716 , 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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