1K2D Immune System date Sep 26, 2001
title Crystal Structure Of The Autoimmune Mhc Class II I-Au Comple Myelin Basic Protein 1-11 At 2.2a
authors X.L.He, C.Radu, E.S.Ward, K.C.Garcia
compound source
Molecule: H-2 Class II Histocompatibility Antigen, A-U Alph
Chain: A
Fragment: Extracellular Alpha-1 And Alpha-2 Domains
Synonym: Mhc Class II I-Au
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227

Molecule: H-2 Class II Histocompatibility Antigen, A-U Beta
Chain: B
Fragment: Extracellular Beta-1 And Beta-2 Domains
Synonym: Mhc Class II I-Au
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227

Molecule: Myelin Basic Protein Peptide With 8 Residue Linke
Chain: P
Fragment: 11 Residue Peptide With 8 Residue Linker Peptide
Synonym: Mbp Peptide
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Of The Mbp Portion Of The Peptide Is Naturally Found In Hom (Human).
symmetry Space Group: C 2 2 21
R_factor 0.248 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.150 110.590 94.840 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand NAG enzyme
related structures by homologous chain: 1MUJ, 1S9V
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au., He XL, Radu C, Sidney J, Sette A, Ward ES, Garcia KC, Immunity 2002 Jul;17(1):83-94. PMID:12150894
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1k2d.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 1K2D
  • CSU: Contacts of Structural Units for 1K2D
  • Likely Quarternary Molecular Structure file(s) for 1K2D
  • Retrieve 1K2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K2D from S2C, [Save to disk]
  • View 1K2D 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 1K2D
  • 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 1K2D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k2da2, region A:1-81 [Jmol] [rasmolscript] [script source]
        - Domain d1k2da1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1k2db2, region B:5-92 [Jmol] [rasmolscript] [script source]
        - Domain d1k2db1, region B:93-190 [Jmol] [rasmolscript] [script source]
  • Fold representative 1k2d 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: [1k2d_P] [1k2d] [1k2d_B] [1k2d_A]
  • SWISS-PROT database: [P14438] [P06344]
  • Domain organization of [HA2U_MOUSE] [HB2U_MOUSE] by SWISSPFAM
  • Domains found in 1K2D: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Other resources with information on 1K2D
  • Community annotation for 1K2D 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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