1WKK Transferase date Jun 01, 2004
title Crystal Structure Of Nucleoside Diphosphate Kinase From Thermus Thermophilus Hb8 In Complex With Gdp
authors S.Takeishi, N.Nakagawa, R.Masui, S.Kuramitsu, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Nucleoside Diphosphate Kinase
Chain: A, B
Ec: 2.7.4.6
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Gene: Ndk
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 63 2 2
R_factor 0.201 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.830 123.830 104.302 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand GDP enzyme Transferase E.C.2.7.4.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1wkk.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 1WKK
  • CSU: Contacts of Structural Units for 1WKK
  • Likely Quarternary Molecular Structure file(s) for 1WKK
  • Retrieve 1WKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WKK from S2C, [Save to disk]
  • View 1WKK 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 1WKK
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1WKK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wkk] [1wkk_B] [1wkk_A]
  • SWISS-PROT database: [Q5SLV5]
  • Domain organization of [NDK_THET8] by SWISSPFAM
  • Domain found in 1WKK: [NDK ] by SMART
  • Other resources with information on 1WKK
  • Community annotation for 1WKK 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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