3D5V Transferase date May 17, 2008
title Crystal Structure Of An Activated (Thr->Asp) Polo-Like Kinas Catalytic Domain.
authors R.A.Elling, R.V.Fucini, M.J.Romanowski
compound source
Molecule: Polo-Like Kinase 1
Chain: A
Fragment: Catalytic Domain
Ec: 2.7.11.21
Engineered: Yes
Mutation: Yes
Organism_scientific: Danio Rerio
Organism_common: Leopard Danio,Zebra Danio,Zebra Fish
Organism_taxid: 7955
Gene: Plk1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1
symmetry Space Group: I 2 3
R_factor 0.234 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.767 134.767 134.767 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand
enzyme Transferase E.C.2.7.11.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands., Elling RA, Fucini RV, Romanowski MJ, Acta Crystallogr D Biol Crystallogr. 2008 Sep;64(Pt 9):909-18. Epub 2008, Aug 13. PMID:18703838
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3d5v.pdb1.gz) 44 Kb
  • CSU: Contacts of Structural Units for 3D5V
  • Likely Quarternary Molecular Structure file(s) for 3D5V
  • Structure Factors (126 Kb)
  • Retrieve 3D5V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D5V from S2C, [Save to disk]
  • Re-refined 3d5v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D5V 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 3D5V
  • 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
  • 3D motif for 3D5V, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d5v] [3d5v_A]
  • SWISS-PROT database: [Q6DRK7]
  • Domain organization of [Q6DRK7_DANRE] by SWISSPFAM
  • Domain found in 3D5V: [S_TKc ] by SMART
  • Other resources with information on 3D5V
  • Community annotation for 3D5V 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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