1S9V Immune System date Feb 05, 2004
title Crystal Structure Of Hla-Dq2 Complexed With Deamidated Gliadin Peptide
authors C.Y.Kim, H.Quarsten, E.Bergseng, C.Khosla, L.M.Sollid
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dq(3) Alpha Chain;
Chain: A, D
Fragment: Residues (-1)-191
Synonym: Hla-Dq2 Alpha Chain, Hla-Dqa10501, Dc-Alpha, Hla- Dca;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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: Pacab3

Molecule: Hla Class II Histocompatibility Antigen, Dq(1) Beta Chain;
Chain: B, E
Fragment: Residues 1-198
Synonym: Hla-Dq2 Beta Chain, Dqb10201, Dc-3 Beta Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
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: Pacab3

Molecule: Alpha-I Gliadin
Chain: C, F
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.110 93.750 102.720 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.22 Å
ligand EDO enzyme
related structures by homologous chain: 1JK8, 1K2D, 1SJH
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


Primary referenceStructural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease., Kim CY, Quarsten H, Bergseng E, Khosla C, Sollid LM, Proc Natl Acad Sci U S A 2004 Mar 23;101(12):4175-9. Epub 2004 Mar 12. PMID:15020763
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (1s9v.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (1s9v.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 1S9V
  • CSU: Contacts of Structural Units for 1S9V
  • Likely Quarternary Molecular Structure file(s) for 1S9V
  • Retrieve 1S9V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S9V from S2C, [Save to disk]
  • View 1S9V 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 1S9V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1S9V, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s9va2, region A:2-84 [Jmol] [rasmolscript] [script source]
        - Domain d1s9va1, region A:85-180 [Jmol] [rasmolscript] [script source]
        - Domain d1s9vb2, region B:3-94 [Jmol] [rasmolscript] [script source]
        - Domain d1s9vb1, region B:95-190 [Jmol] [rasmolscript] [script source]
        - Domain d1s9vd2, region D:2-84 [Jmol] [rasmolscript] [script source]
        - Domain d1s9vd1, region D:85-178 [Jmol] [rasmolscript] [script source]
        - Domain d1s9ve2, region E:3-94 [Jmol] [rasmolscript] [script source]
        - Domain d1s9ve1, region E:95-190 [Jmol] [rasmolscript] [script source]
  • Fold representative 1s9v 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: [1s9v] [1s9v_F] [1s9v_B] [1s9v_C] [1s9v_A] [1s9v_E] [1s9v_D]
  • SWISS-PROT database: [P01909] [P01920]
  • Domain organization of [DQA1_HUMAN] [DQB1_HUMAN] by SWISSPFAM
  • Domains found in 1S9V: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1S9V with the sequences similar proteins can be viewed for 1S9V's classification [DQA1_HUMAN] [DQB1_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 [DQA1_HUMAN] [DQB1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1S9V
  • Community annotation for 1S9V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science