3ZE4 Transferase date Dec 03, 2012
title Crystal Structure Of The Integral Membrane Diacylglycerol Ki Wild-Type
authors D.Li, J.A.Lyons, V.E.Pye, L.Vogeley, D.Aragao, M.Caffrey
compound source
Molecule: Diacylglycerol Kinase
Chain: A, B, C
Synonym: Dagk, Diglyceride Kinase, Dgk
Engineered: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Wh1061
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrchisb
Expression_system_plasmid: Ptrchisb_dgka_wild-Type
Other_details: The Wild-Type Gene Was Synthesized Based On Nucleotide Sequence Of Escherichia Coli K12, With Additiona Nucleotides Encoding His Tag Sequences At The N-Terminus.
symmetry Space Group: P 31 2 1
R_factor 0.285 R_Free 0.312
length a length b length c angle alpha angle beta angle gamma
74.970 74.970 196.900 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.70 Å
enzyme Transferase E.C. BRENDA
A, C, B

Primary referenceCrystal structure of the integral membrane diacylglycerol kinase., Li D, Lyons JA, Pye VE, Vogeley L, Aragao D, Kenyon CP, Shah ST, Doherty C, Aherne M, Caffrey M, Nature. 2013 May 23;497(7450):521-4. doi: 10.1038/nature12179. Epub 2013 May 15. PMID:23676677
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (3ze4.pdb1.gz) 107 Kb
  • CSU: Contacts of Structural Units for 3ZE4
  • Structure Factors (89 Kb)
  • Retrieve 3ZE4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZE4 from S2C, [Save to disk]
  • Re-refined 3ze4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZE4 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 3ZE4
  • 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 3ZE4, from MSDmotif at EBI
  • Fold representative 3ze4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ze4] [3ze4_B] [3ze4_C] [3ze4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ZE4
  • Community annotation for 3ZE4 at PDBWiki (http://pdbwiki.org)

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