1JXV Transferase date Sep 10, 2001
title Crystal Structure Of Human Nucleoside Diphosphate Kinase A
authors K.Min, H.K.Song, C.Chang, S.Y.Kim, K.J.Lee, S.W.Suh
compound source
Molecule: Nucleoside Diphosphate Kinase A
Chain: A, B, C, D, E, F
Ec: 2.7.4.6
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nm23-H1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3c
symmetry Space Group: P 1 21 1
R_factor 0.207 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.210 78.110 82.290 90.00 101.33 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand
enzyme Transferase E.C.2.7.4.6 BRENDA
related structures by homologous chain: 1NDK, 2BEF
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • deoxyribonuclease activity


  • Primary referenceCrystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor., Min K, Song HK, Chang C, Kim SY, Lee KJ, Suh SW, Proteins 2002 Feb 15;46(3):340-2. PMID:11835509
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (1jxv.pdb1.gz) 145 Kb
  • CSU: Contacts of Structural Units for 1JXV
  • Likely Quarternary Molecular Structure file(s) for 1JXV
  • Structure Factors (417 Kb)
  • Retrieve 1JXV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JXV from S2C, [Save to disk]
  • Re-refined 1jxv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JXV 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 1JXV
  • 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 1JXV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jxva_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jxvb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1jxvc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1jxvd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1jxve_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1jxvf_, region F [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: [1jxv_C] [1jxv_A] [1jxv_B] [1jxv_E] [1jxv_F] [1jxv] [1jxv_D]
  • SWISS-PROT database: [P15531]
  • Domain organization of [NDKA_HUMAN] by SWISSPFAM
  • Domain found in 1JXV: [NDK ] by SMART
  • Other resources with information on 1JXV
  • Community annotation for 1JXV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science