1YRK Protein Binding date Feb 03, 2005
title The C2 Domain Of Pkc Is A New Phospho-Tyrosine Binding Domain
authors C.H.Benes, N.Wu, A.E.Elia, T.Dharia, L.C.Cantley, S.P.Soltoff
compound source
Molecule: Protein Kinase C, Delta Type
Chain: A
Fragment: C2 Domain, Residues 1-123
Synonym: Npkc-Delta
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: 13-Residue Peptide
Chain: B
Engineered: Yes
Other_details: An Optimal Peptide Motif For C2 Binding

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.272 41.856 88.463 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ACY, PTR enzyme
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Primary referenceC2 can do it, too., Sondermann H, Kuriyan J, Cell 2005 Apr 22;121(2):158-60. PMID:15851022
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (1yrk.pdb1.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 1YRK
  • CSU: Contacts of Structural Units for 1YRK
  • Likely Quarternary Molecular Structure file(s) for 1YRK
  • Structure Factors (124 Kb)
  • Retrieve 1YRK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YRK from S2C, [Save to disk]
  • Re-refined 1yrk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YRK 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 1YRK
  • 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 1YRK, from MSDmotif at EBI
  • Fold representative 1yrk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yrk_A] [1yrk] [1yrk_B]
  • SWISS-PROT database: [Q05655]
  • Domain organization of [KPCD_HUMAN] by SWISSPFAM
  • Domain found in 1YRK: [C2 ] by SMART
  • Alignments of the sequence of 1YRK with the sequences similar proteins can be viewed for 1YRK's classification [KPCD_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 [KPCD_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YRK
  • Community annotation for 1YRK 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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