3DY7 Transferase date Jul 25, 2008
title X-Ray Structure Of The Human Mitogen-Activated Protein Kinase Kinase 1 (Mek1) In A Complex With Ligand And Mgatp
authors J.F.Ohren, A.Pavlovsky, E.Zhang
compound source
Molecule: Dual Specificity Mitogen-Activated Protein Kinase Kinase 1;
Chain: A
Fragment: Protein Kinase Domain, Unp Residues 62-393
Synonym: Map Kinase Kinase 1, Mapkk 1, Erk Activator Kinase 1, Mapkerk Kinase 1, Mek1;
Ec: 2.7.12.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map2k1, Mek1, Prkmk1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: P 62
R_factor 0.247 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.754 81.754 128.893 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand 1CX, ATP, MG BindingDB enzyme Transferase E.C.2.7.12.2 BRENDA
Primary referenceBeyond the MEK-pocket: can current MEK kinase inhibitors be utilized to synthesize novel type III NCKIs? Does the MEK-pocket exist in kinases other than MEK?, Tecle H, Shao J, Li Y, Kothe M, Kazmirski S, Penzotti J, Ding YH, Ohren J, Moshinsky D, Coli R, Jhawar N, Bora E, Jacques-O'Hagan S, Wu J, Bioorg Med Chem Lett. 2009 Jan 1;19(1):226-9. Epub 2008 Oct 31. PMID:19019675
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (3dy7.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3DY7
  • CSU: Contacts of Structural Units for 3DY7
  • Likely Quarternary Molecular Structure file(s) for 3DY7
  • Structure Factors (195 Kb)
  • Retrieve 3DY7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DY7 from S2C, [Save to disk]
  • Re-refined 3dy7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DY7 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 3DY7
  • 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 3DY7, from MSDmotif at EBI
  • Fold representative 3dy7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dy7] [3dy7_A]
  • SWISS-PROT database: [Q02750]
  • Domain organization of [MP2K1_HUMAN] by SWISSPFAM
  • Domain found in 3DY7: [S_TKc ] by SMART
  • Alignments of the sequence of 3DY7 with the sequences similar proteins can be viewed for 3DY7's classification [MP2K1_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 [MP2K1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3DY7
  • Community annotation for 3DY7 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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