OCA Atlas for 1S9V

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

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

Gene
Ontology

Chain	Function	Process	Component
A, D
E, B

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.

Visual 3D analysis of 1S9V

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server 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]

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

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.

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