4NNY Immune System Antigen date Nov 19, 2013
title Crystal Structure Of Non-Phosphorylated Form Of Pkd2 Phospho Bound To Hla-A2
authors F.Mohammed, D.H.Stones, B.E.Willcox
compound source
Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha
Chain: A
Fragment: Extracellular Domain (Unp Residues 25-298)
Synonym: Mhc Class I Antigen A2, Class I Histocompatibilit A0201;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-A, Hlaa
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Unp Residues 21-119
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgmt7

Molecule: Serinethreonine-Protein Kinase D2
Chain: C
Fragment: Peptide (Unp Residues 526-534)
Synonym: Npkc-D2
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.400 79.800 110.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CD, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
B
  • cellular response to iron io...

  • Primary referenceThe antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status., Mohammed F, Stones DH, Zarling AL, Willcox CR, Shabanowitz J, Cummings KL, Hunt DF, Cobbold M, Engelhard VH, Willcox BE, Oncotarget. 2017 Apr 8;8(33):54160-54172. doi: 10.18632/oncotarget.16952., eCollection 2017 Aug 15. PMID:28903331
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (4nny.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 4NNY
  • CSU: Contacts of Structural Units for 4NNY
  • Structure Factors (631 Kb)
  • Retrieve 4NNY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NNY from S2C, [Save to disk]
  • Re-refined 4nny structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NNY 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 4NNY
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  • 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 4NNY, from MSDmotif at EBI
  • Fold representative 4nny from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nny_B] [4nny] [4nny_A] [4nny_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NNY: [IGc1 ] by SMART
  • Other resources with information on 4NNY
  • Community annotation for 4NNY at PDBWiki (http://pdbwiki.org)

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