1S9X Immune System date Feb 05, 2004
title Crystal Structure Analysis Of Ny-Eso-1 Epitope Analogue, Sllmwitqa, In Complex With Hla-A2
authors A.I.Webb, M.A.Dunstone, W.Chen, M.I.Aguilar, Q.Chen, L.Chang, L.Kjer-Nielsen, T.Beddoe, J.Mccluskey, J.Rossjohn, A.W.Purcell
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain;
Chain: A
Fragment: Extracellular Domains Alpha1, Alpha2, Alpha3
Synonym: Hla-A2, Mhc Class I Antigen A2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Beta-2-Microglobulin
Chain: B
Synonym: Beta2 Microglobulin, Hdcma22p
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ny-Eso-1 Peptide Analogue S9a
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide
symmetry Space Group: P 21 3
R_factor 0.230 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
117.950 117.950 117.950 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand SO4 enzyme
related structures by homologous chain: 1BD2, 1MI5, 1R3H
  • cellular response to iron io...

  • Primary referenceFunctional and structural characteristics of NY-ESO-1-related HLA A2-restricted epitopes and the design of a novel immunogenic analogue., Webb AI, Dunstone MA, Chen W, Aguilar MI, Chen Q, Jackson H, Chang L, Kjer-Nielsen L, Beddoe T, McCluskey J, Rossjohn J, Purcell AW, J Biol Chem 2004 May 28;279(22):23438-46. Epub 2004 Mar 5. PMID:15004033
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (1s9x.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1S9X
  • CSU: Contacts of Structural Units for 1S9X
  • Likely Quarternary Molecular Structure file(s) for 1S9X
  • Retrieve 1S9X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S9X from S2C, [Save to disk]
  • View 1S9X 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 1S9X
  • 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 1S9X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s9xa2, region A:1-181 [Jmol] [rasmolscript] [script source]
        - Domain d1s9xa1, region A:182-274 [Jmol] [rasmolscript] [script source]
        - Domain d1s9xb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1s9x 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: [1s9x_A] [1s9x_C] [1s9x_B] [1s9x]
  • SWISS-PROT database: [P01892] [P61769]
  • Domain organization of [1A02_HUMAN] [B2MG_HUMAN] by SWISSPFAM
  • Domain found in 1S9X: [IGc1 ] by SMART
  • Other resources with information on 1S9X
  • Community annotation for 1S9X 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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