1KDO Transferase date Nov 13, 2001
title Cytidine Monophosphate Kinase From E. Coli In Complex With C Monophosphate
authors T.Bertrand, P.Briozzo, L.Assairi, A.Ofiteru, N.Bucurenci, H.Munie Lehmann, B.Golinelli-Pimpaneau, O.Barzu, A.M.Gilles
compound source
Molecule: Cytidylate Kinase
Chain: A, B
Synonym: Cytidine Monophosphate Kinase; Ck; Cmp Kinase
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Cmk
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phsp210
symmetry Space Group: P 21 21 21
R_factor 0.202 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
74.087 75.736 77.988 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand C, SO4 enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1CKE, 1KDT
A, B
  • cytidylate kinase activity

  • Primary referenceSugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme., Bertrand T, Briozzo P, Assairi L, Ofiteru A, Bucurenci N, Munier-Lehmann H, Golinelli-Pimpaneau B, Barzu O, Gilles AM, J Mol Biol 2002 Feb 1;315(5):1099-110. PMID:11827479
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (1kdo.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (1kdo.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 1KDO
  • CSU: Contacts of Structural Units for 1KDO
  • Likely Quarternary Molecular Structure file(s) for 1KDO
  • Retrieve 1KDO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KDO from S2C, [Save to disk]
  • View 1KDO 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 1KDO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KDO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kdoa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kdob_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1kdo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1kdo_B] [1kdo] [1kdo_A]
  • SWISS-PROT database: [P0A6I0]
  • Domain organization of [KCY_ECOLI] by SWISSPFAM
  • Other resources with information on 1KDO
  • Community annotation for 1KDO 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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