3KD6 Transferase date Oct 22, 2009
title Crystal Structure Of Nucleoside Kinase From Chlorobium Tepid Complex With Amp
authors L.Satyanarayana, S.K.Burley, S.Swaminathan, New York Sgx Resear For Structural Genomics (Nysgxrc)
compound source
Molecule: Carbohydrate Kinase, Pfkb Family
Chain: A, B
Engineered: Yes
 Organism_scientific: Chlorobaculum Tepidum
Organism_taxid: 1097
Gene: Ct0976
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Codon+Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psgx32 (Bc)
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.014 89.797 64.827 90.00 92.90 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand AMP, GOL, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (3kd6.pdb1.gz) 99 Kb
  • Biological Unit Coordinates (3kd6.pdb2.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 3KD6
  • CSU: Contacts of Structural Units for 3KD6
  • Structure Factors (681 Kb)
  • Retrieve 3KD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KD6 from S2C, [Save to disk]
  • Re-refined 3kd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3KD6 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 3KD6
  • 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
  • 3D motif for 3KD6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kd6] [3kd6_A] [3kd6_B]
  • SWISS-PROT database: [Q8KDR9]
  • Domain organization of [Q8KDR9_CHLTE] by SWISSPFAM
    • Other resources with information on 3KD6
  • Community annotation for 3KD6 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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