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 Diffraction	resolution	2.22 Å
ligand	EDO	enzyme
related structures	by homologous chain: 1JK8, 1K2D, 1SJH
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [1s9v_B] [1s9v_C] [1s9v_D] [1s9v_E] [1s9v_F] 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)

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