1W1D Transferase date Jun 21, 2004
title Crystal Structure Of The Pdk1 Pleckstrin Homology (Ph) Domain Bound To Inositol (1,3,4,5)-Tetrakisphosphate
authors D.Komander, M.Deak, D.R.Alessi, D.M.F.Van Aalten
compound source
Molecule: 3-Phosphoinositide Dependent Protein Kinase-1
Chain: A
Fragment: Pleckstrin Homology Domain, Residues 409-556
Synonym: Hpdk1
Ec: 2.7.1.37
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pgex
symmetry Space Group: P 1 21 1
R_factor 0.145 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.399 58.922 36.578 90.00 101.48 90.00
method X-Ray Diffractionresolution 1.5 Å
ligand 4IP, AU, GOL enzyme Transferase E.C.2.7.1.37 BRENDA
note 1W1D is a representative structure
related structures by homologous chain: 1W1G
Primary referenceStructural insights into the regulation of PDK1 by phosphoinositides and inositol phosphates., Komander D, Fairservice A, Deak M, Kular GS, Prescott AR, Peter Downes C, Safrany ST, Alessi DR, van Aalten DM, EMBO J. 2004 Oct 13;23(20):3918-28. Epub 2004 Sep 30. PMID:15457207
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1w1d.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 1W1D
  • CSU: Contacts of Structural Units for 1W1D
  • Likely Quarternary Molecular Structure file(s) for 1W1D
  • Structure Factors (154 Kb)
  • Retrieve 1W1D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W1D from S2C, [Save to disk]
  • Re-refined 1w1d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1W1D 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 1W1D
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1W1D from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1W1D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w1da_, region A [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1w1d] [1w1d_A]
  • SWISS-PROT database: [O15530]
  • Domain organization of [PDPK1_HUMAN] by SWISSPFAM
    • Other resources with information on 1W1D
  • Community annotation for 1W1D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science