4C58 Transferase date Sep 10, 2013
title Structure Of Gak Kinase In Complex With Nanobody (Nbgak_4)
authors A.Chaikuad, T.Keates, C.K.Allerston, O.Gileadi, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Knapp, S.Muller-Knapp
compound source
Molecule: Cyclin-G-Associated Kinase
Chain: A
Fragment: Kinase Domain, Residues 27-351
Synonym: Gak
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: Nanobody
Chain: B

Synthetic: Yes
Organism_scientific: Lama Glama
Organism_common: Llama
Organism_taxid: 9844
symmetry Space Group: C 1 2 1
R_factor 0.17929 R_Free 0.24172
length a length b length c angle alpha angle beta angle gamma
156.866 37.430 76.010 90.00 108.48 90.00
method X-Ray Diffractionresolution 2.16 Å
ligand 824, EDO enzyme Transferase E.C. BRENDA

Primary referenceStructure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies., Chaikuad A, Keates T, Vincke C, Kaufholz M, Zenn M, Zimmermann B, Gutierrez C, Zhang RG, Hatzos-Skintges C, Joachimiak A, Muyldermans S, Herberg FW, Knapp S, Muller S, Biochem J. 2014 Apr 1;459(1):59-69. doi: 10.1042/BJ20131399. PMID:24438162
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (4c58.pdb1.gz) 184 Kb
  • Biological Unit Coordinates (4c58.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 4C58
  • CSU: Contacts of Structural Units for 4C58
  • Structure Factors (334 Kb)
  • Retrieve 4C58 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C58 from S2C, [Save to disk]
  • Re-refined 4c58 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C58 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 4C58
  • 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 4C58, from MSDmotif at EBI
  • Fold representative 4c58 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c58_B] [4c58_A] [4c58]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4C58: [IGv] [STYKc ] by SMART
  • Other resources with information on 4C58
  • Community annotation for 4C58 at PDBWiki (http://pdbwiki.org)

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