3BGM Immune System date Nov 27, 2007
title Crystal Structure Of Pkd2 Phosphopeptide Bound To Human Class I Mhc Hla-A2
authors F.Mohammed, M.Cobbold, A.L.Zarling, M.Salim, G.A.Barrett-Wilt, J.Shabanowitz, D.F.Hunt, V.H.Engelhard, B.E.Willcox
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain;
Chain: A
Fragment: Alpha-1, Alpha-2, Alpha-3
Synonym: Mhc Class I Antigen A2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A, Hlaa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Beta-2-Microglobulin
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Nonameric Peptide From Serinethreonine-Protein Kinase D2;
Chain: C
Fragment: Unp Residues 526-534
Synonym: Npkc-D2
Engineered: Yes

Synthetic: Yes
Other_details: Commercial Synthesis
symmetry Space Group: C 1 2 1
R_factor 0.202 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.800 54.800 75.800 90.00 105.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EDO, SEP enzyme
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referencePhosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self., Mohammed F, Cobbold M, Zarling AL, Salim M, Barrett-Wilt GA, Shabanowitz J, Hunt DF, Engelhard VH, Willcox BE, Nat Immunol. 2008 Nov;9(11):1236-43. Epub 2008 Oct 5. PMID:18836451
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3bgm.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3BGM
  • CSU: Contacts of Structural Units for 3BGM
  • Likely Quarternary Molecular Structure file(s) for 3BGM
  • Structure Factors (908 Kb)
  • Retrieve 3BGM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BGM from S2C, [Save to disk]
  • Re-refined 3bgm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BGM 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 3BGM
  • 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 3BGM, from MSDmotif at EBI
  • Fold representative 3bgm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bgm_A] [3bgm_C] [3bgm] [3bgm_B]
  • SWISS-PROT database: [P01892] [P61769] [Q9BZL6]
  • Domain organization of [1A02_HUMAN] [B2MG_HUMAN] [KPCD2_HUMAN] by SWISSPFAM
  • Domain found in 3BGM: [IGc1 ] by SMART
  • Other resources with information on 3BGM
  • Community annotation for 3BGM 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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