4D2V Transferase date May 13, 2014
title Structure Of Melk In Complex With Inhibitors
authors C.N.Johnson, V.Berdini, L.Beke, P.Bonnet, D.Brehmer, J.E.Coyle, P. M.Frederickson, E.J.E.Freyne, R.A.H.J.Gilissen, C.C.F.Hamlett, L.Meerpoel, R.Mcmenamin, S.Patel, D.C.Rees, A.Sharff, F.Sommen, T J.T.M.Linders
compound source
Molecule: Maternal Embryonic Leucine Zipper Kinase
Chain: A, C, B, D
Synonym: Hmelk, Protein Kinase Eg3, Peg3 Kinase, Protein Ki Pk38, Hpk38, Tyrosine-Protein Kinase Melk, Hmelk, Protein Eg3, Peg3 Kinase, Protein Kinase Pk38, Hpk38, Tyrosine-Pro Kinase Melk, Melk;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Other_details: Image Clone
symmetry Space Group: P 1
R_factor 0.2913 R_Free 0.357
length a length b length c angle alpha angle beta angle gamma
66.650 75.860 79.070 86.08 69.45 89.87
method X-Ray Diffractionresolution 2.45 Å
ligand 45R enzyme Transferase E.C. BRENDA
A, D, C, B

Primary referenceFragment-based discovery of type I inhibitors of maternal embryonic leucine zipper kinase., Johnson CN, Berdini V, Beke L, Bonnet P, Brehmer D, Coyle JE, Day PJ, Frederickson M, Freyne EJ, Gilissen RA, Hamlett CC, Howard S, Meerpoel L, McMenamin R, Patel S, Rees DC, Sharff A, Sommen F, Wu T, Linders JT, ACS Med Chem Lett. 2014 May 23;6(1):25-30. doi: 10.1021/ml5001245. eCollection, 2015 Jan 8. PMID:25589925
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (460 Kb) [Save to disk]
  • Biological Unit Coordinates (4d2v.pdb1.gz) 229 Kb
  • Biological Unit Coordinates (4d2v.pdb2.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 4D2V
  • CSU: Contacts of Structural Units for 4D2V
  • Structure Factors (903 Kb)
  • Retrieve 4D2V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D2V from S2C, [Save to disk]
  • Re-refined 4d2v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D2V 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 4D2V
  • 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 4D2V, from MSDmotif at EBI
  • Fold representative 4d2v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d2v_D] [4d2v_C] [4d2v] [4d2v_A] [4d2v_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4D2V: [S_TKc ] by SMART
  • Other resources with information on 4D2V
  • Community annotation for 4D2V at PDBWiki (http://pdbwiki.org)

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