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, D, G, J
Fragment: Secreted Extracellular Domains
Synonym: Dra, Drb1 01010
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Plasma
Tissue: Lymphoid
Cellular_location: Plasma Membrane
Gene: Dra0101, Drb10101
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pvl1392-Based

Molecule: Hla-Dr1 Class II Histocompatibility Protein
Chain: B, E, H, K
Fragment: Secreted Extracellular Domains
Synonym: Dra, Drb1 01010
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Plasma
Tissue: Lymphoid
Cellular_location: Plasma Membrane
Gene: Dra0101, Drb10101
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.216 R_Free 0.279
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
Primary referenceThe class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding., Murthy VL, Stern LJ, Structure 1997 Oct 15;5(10):1385-96. PMID:9351812
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (263 Kb) [Save to disk]
  • Biological Unit Coordinates (1aqd.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (1aqd.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (1aqd.pdb3.gz) 68 Kb
  • Biological Unit Coordinates (1aqd.pdb4.gz) 68 Kb
  • CSU: Contacts of Structural Units for 1AQD
  • Likely Quarternary Molecular Structure file(s) for 1AQD
  • Structure Factors (676 Kb)
  • Retrieve 1AQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1AQD from S2C, [Save to disk]
  • Re-refined 1aqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1AQD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1AQD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1AQD, from MSDmotif at EBI
  • Genome occurence of 1AQD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1aqda2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1aqda1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdb2, region B:4-92 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdd2, region D:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdd1, region D:82-179 [Jmol] [rasmolscript] [script source]
        - Domain d1aqde2, region E:4-92 [Jmol] [rasmolscript] [script source]
        - Domain d1aqde1, region E:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdg2, region G:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdg1, region G:82-179 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdh2, region H:4-92 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdh1, region H:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdj2, region J:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdj1, region J:82-179 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdk2, region K:4-92 [Jmol] [rasmolscript] [script source]
        - Domain d1aqdk1, region K:93-191 [Jmol] [rasmolscript] [script source]
  • Fold representative 1aqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1aqd_K] [1aqd_F] [1aqd_B] [1aqd_A] [1aqd_E] [1aqd_L] [1aqd] [1aqd_G] [1aqd_D] [1aqd_H] [1aqd_I] [1aqd_J] [1aqd_C]
  • SWISS-PROT database: [P01892] [P04229] [P01903]
  • Domain organization of [1A02_HUMAN] [2B11_HUMAN] [DRA_HUMAN] by SWISSPFAM
  • Domains found in 1AQD: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1AQD
  • Community annotation for 1AQD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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