1JK8 Immune System date Jul 11, 2001
title Crystal Structure Of A Human Insulin Peptide-Hla-Dq8 Complex
authors K.H.Lee, K.W.Wucherpfennig, D.C.Wiley
compound source
Molecule: Mhc Class II Hla-Dq8
Chain: A
Fragment: Alpha Chain (Dqa10301)
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_vector_type: Baculovirus

Molecule: Mhc Class II Hla-Dq8
Chain: B
Fragment: Beta Chain (Dqb10302)
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_vector_type: Baculovirus

Molecule: Insulin B Peptide
Chain: C
Fragment: Peptide (9-Shlvealylvcgerg-23)
Engineered: Yes

Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized. The Of This Peptide Occurs Naturally In Humans (Homo Sapiens).
symmetry Space Group: P 1 21 1
R_factor 0.224 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.034 42.862 87.467 90.00 102.48 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG enzyme
related structures by homologous chain: 1I3R, 1KTD, 1S9V, 2IAD
Primary referenceStructure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes., Lee KH, Wucherpfennig KW, Wiley DC, Nat Immunol 2001 Jun;2(6):501-7. PMID:11376336
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1jk8.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1JK8
  • CSU: Contacts of Structural Units for 1JK8
  • Likely Quarternary Molecular Structure file(s) for 1JK8
  • Structure Factors (149 Kb)
  • Retrieve 1JK8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JK8 from S2C, [Save to disk]
  • Re-refined 1jk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JK8 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 1JK8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1JK8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jk8a2, region A:2-84 [Jmol] [rasmolscript] [script source]
        - Domain d1jk8a1, region A:85-181 [Jmol] [rasmolscript] [script source]
        - Domain d1jk8b2, region B:3-94 [Jmol] [rasmolscript] [script source]
        - Domain d1jk8b1, region B:95-192 [Jmol] [rasmolscript] [script source]
  • Fold representative 1jk8 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: [1jk8] [1jk8_C] [1jk8_B] [1jk8_A]
  • SWISS-PROT database: [P01909] [P01920]
  • Domain organization of [DQA1_HUMAN] [DQB1_HUMAN] by SWISSPFAM
  • Domains found in 1JK8: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1JK8 with the sequences similar proteins can be viewed for 1JK8'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 1JK8
  • Community annotation for 1JK8 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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