3DBD	Transferase	date	May 31, 2008
title	Crystal Structure Of An Activated (Thr->Asp) Polo-Like Kinas Catalytic Domain In Complex With Compound 094
authors	R.A.Elling, K.J.Barr, M.J.Romanowski
compound		source
Molecule: Polo-Like Kinase 1 Chain: A Fragment: Plk1 Kinase Domain Ec: 2.7.11.21 Engineered: Yes Mutation: Yes		Organism_scientific: Danio Rerio Organism_common: Zebrafish Organism_taxid: 7955 Gene: Plk1 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3) Star Codon+ Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex6p-1
symmetry	Space Group: I 2 3	R_factor 0.250 R_Free 0.276
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.267 135.267 135.267 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.05 Å
ligand	3FR	enzyme	Transferase E.C.2.7.11.21 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Design and synthesis of 2-amino-pyrazolopyridines as Polo-like kinase 1 inhibitors., Fucini RV, Hanan EJ, Romanowski MJ, Elling RA, Lew W, Barr KJ, Zhu J, Yoburn JC, Liu Y, Fahr BT, Fan J, Lu Y, Pham P, Choong IC, Vanderporten EC, Bui M, Purkey HE, Evanchik MJ, Yang W, Bioorg Med Chem Lett. 2008 Aug 29. PMID:18793847

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk] Biological Unit Coordinates (3dbd.pdb1.gz) 43 Kb LPC: Ligand-Protein Contacts for 3DBD CSU: Contacts of Structural Units for 3DBD Likely Quarternary Molecular Structure file(s) for 3DBD Structure Factors (64 Kb) Retrieve 3DBD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DBD from S2C, [Save to disk] Re-refined 3dbd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DBD 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 3DBD

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 3DBD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dbd] [3dbd_A] SWISS-PROT database: [Q4KMI8] Domain organization of [Q4KMI8_DANRE] by SWISSPFAM Domain found in 3DBD: [S_TKc ] by SMART

Other resources with information on 3DBD

Community annotation for 3DBD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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