3BGZ Transferase date Nov 27, 2007
title Human Pim-1 Kinase In Complex With Diphenyl Indole Inhibitor Vx3
authors M.D.Jacobs
compound source
Molecule: Proto-Oncogene Serinethreonine-Protein Kinase Pim-1;
Chain: A
Fragment: Kinase Domain Residues 92-404
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pim1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21de3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbev1
symmetry Space Group: P 65
R_factor 0.194 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.130 98.130 80.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand SEP, VX3 BindingDB enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDocking study yields four novel inhibitors of the protooncogene Pim-1 kinase., Pierce AC, Jacobs M, Stuver-Moody C, J Med Chem. 2008 Mar 27;51(6):1972-5. Epub 2008 Feb 22. PMID:18290603
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3bgz.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 3BGZ
  • CSU: Contacts of Structural Units for 3BGZ
  • Likely Quarternary Molecular Structure file(s) for 3BGZ
  • Structure Factors (204 Kb)
  • Retrieve 3BGZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BGZ from S2C, [Save to disk]
  • Re-refined 3bgz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BGZ 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 3BGZ
  • 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 3BGZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bgz] [3bgz_A]
  • SWISS-PROT database: [P11309]
  • Domain organization of [PIM1_HUMAN] by SWISSPFAM
  • Domain found in 3BGZ: [S_TKc ] by SMART
  • Other resources with information on 3BGZ
  • Community annotation for 3BGZ 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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