1OKY Transferase date Aug 01, 2003
title Structure Of Human Pdk1 Kinase Domain In Complex With Staurosporine
authors D.Komander, G.S.Kular, D.R.Alessi, D.M.F.Van Aalten
compound source
Molecule: 3-Phosphoinositide Dependent Protein Kinase 1
Chain: A
Fragment: Kinase Domain, Residues 51-360
Synonym: Hpdk1
Ec: 2.7.1.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Sf21
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac1
Other_details: Baculovirus Infected
symmetry Space Group: P 32 2 1
R_factor 0.219 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.172 124.172 47.314 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.3 Å
ligand GOL, SEP, SO4, STU BindingDB enzyme Transferase E.C.2.7.1.37 BRENDA
related structures by homologous chain: 1UU8, 1Z5M
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for UCN-01 (7-hydroxystaurosporine) specificity and PDK1 (3-phosphoinositide-dependent protein kinase-1) inhibition., Komander D, Kular GS, Bain J, Elliott M, Alessi DR, Van Aalten DM, Biochem J. 2003 Oct 15;375(Pt 2):255-62. PMID:12892559
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (1oky.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 1OKY
  • CSU: Contacts of Structural Units for 1OKY
  • Likely Quarternary Molecular Structure file(s) for 1OKY
  • Structure Factors (135 Kb)
  • Retrieve 1OKY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OKY from S2C, [Save to disk]
  • Re-refined 1oky structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OKY 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 1OKY
  • 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 1OKY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1okya_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1oky 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: [1oky] [1oky_A]
  • SWISS-PROT database: [O15530]
  • Domain organization of [PDPK1_HUMAN] by SWISSPFAM
  • Domain found in 1OKY: [S_TKc ] by SMART
  • Alignments of the sequence of 1OKY with the sequences similar proteins can be viewed for 1OKY's classification [PDPK1_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 [PDPK1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1OKY
  • Community annotation for 1OKY 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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