1PAE Transferase date May 14, 2003
title Nucleoside Diphosphate Kinase
authors M.P.Strub, F.Hoh, J.F.Sanchez, J.M.Strub, A.Bock, A.Aumelas, C.D
compound source
Molecule: Nucleoside Diphosphate Kinase, Cytosolic
Chain: X
Synonym: Ndk, Ndp Kinase
Ec: 2.7.4.6
Engineered: Yes
Mutation: Yes
Organism_scientific: Dictyostelium Discoideum
Organism_taxid: 44689
Gene: Ndk
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Selb::Kan Cys51e
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 63 2 2
R_factor 0.182 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.633 76.633 106.510 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE, SE enzyme Transferase E.C.2.7.4.6 BRENDA
related structures by homologous chain: 1B99, 1HIY
Gene
Ontology
ChainFunctionProcessComponent
X


Primary referenceSelenomethionine and selenocysteine double labeling strategy for crystallographic phasing., Strub MP, Hoh F, Sanchez JF, Strub JM, Bock A, Aumelas A, Dumas C, Structure. 2003 Nov;11(11):1359-67. PMID:14604526
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (1pae.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 1PAE
  • CSU: Contacts of Structural Units for 1PAE
  • Likely Quarternary Molecular Structure file(s) for 1PAE
  • Structure Factors (68 Kb)
  • Retrieve 1PAE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PAE from S2C, [Save to disk]
  • Re-refined 1pae structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PAE 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 1PAE
  • 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 1PAE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1paex_, region X [Jmol] [rasmolscript] [script source]
  • 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: [1pae] [1pae_X]
  • SWISS-PROT database: [P22887]
  • Domain organization of [NDKC_DICDI] by SWISSPFAM
  • Domain found in 1PAE: [NDK ] by SMART
  • Other resources with information on 1PAE
  • Community annotation for 1PAE 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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