Nucleoside diphosphate kinase

spinqualitylabelsall models Human nucleoside diphosphate kinase complex with ADP, phosphate, TRIS and Ca+2 ion (green) (PDB entry 1ucn) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function Nucleoside diphosphate kinase (NDK) catalyzes the exchange of phosphate between nucleoside triphosphate and nucleoside diphosphate. This reaction is a multi-step reaction which is used for the synthesis of nucleoside triphosphates other than ATP. NDK provides nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerization. Disease NDKB deficiency causes diabetes-like vascular pathology. Structural highlights The biological assembly of Human nucleoside diphosphate kinase is homohexamer. The NDK-adenine structure shows the two reaction products: ADP and phosphate. Ca coordination site. Water molecules shown as red spheres.

3D structures of nucleoside diphosphate kinase

Updated on 15-August-2018

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• Nucleoside diphosphate kinase
  • 1ndk, 1npk, 1s5z – DdNDK – Dictyostelium discoideum
    
  • 1nlk, 1nsp - DdNDK with phosphohistidine intermediate
    
  • 1leo, 1ncl, 1hlw, 1hhq, 1pae, 4c6a - DdNDK (mutant)
    
  • 2nck – MxNDK – Myxococcus xanthus
    
  • 1ndl, 3wx8 – DmNDK – Drosophila melanogaster
    
  • 1nsq - DmNDK with phosphohistidine intermediate
    
  • 1nsk, 1jxv, 3l7u, 4eno - hNDK A – human
    
  • 1ehw - hNDK 4 (mutant)
    
  • 3bbc - hNDK B (mutant)
    
  • 1k44, 4anc – MtNDK – Mycobacterium tuberculosis
    
  • 4and, 4ane - MtNDK (mutant)
    
  • 1nb2 - NDK - Virgibacillus halodenitrificans
    
  • 1xiq - NDK A – Plasmodium falciparum
    
  • 1w7w - NDK – pea
    
  • 1u8w - AtNDK I – Arabidopsis thaliana
    
  • 1s57 - AtNDK II
    
  • 1pku - NDK I – rice
    
  • 1wkj - TtNDK – Thermus thermophilus
    
  • 1xqi - NDK (mutant) – Pyrobaculum aerophilum
    
  • 2az1 - HsNDK – Halobacterium salinarum
    
  • 2hur - NDK – Escherichia coli
    
  • 3b54 - NDK – yeast
    
  • 2vu5 - NDK – Bacillus anthracis
    
  • 2zua - NDK – Haloarcula quadrata
    
  • 3mpd - NDK – Encephalitozoon cuniculi
    
  • 3pj9 - NDK – Campylobacter jejuni
    
  • 3r9l - NDK – Giardia lamblia
    
  • 3ngr, 3ngs - LmNDK – Leishmania major
    
  • 5c7p, 5caa, 5cab - LmNDK (mutant)
    
  • 4kpc - NDK – Leishmania braziliensis
    
  • 5go1 - NDK – Leishmania amazonensis
    
  • 3prv - NDK – Trypanosoma cruzi
    
  • 3q83 - SaNDK – Staphylococcus aureus
    
  • 4di6 - BbNDK – Borrelia burgdorferi
    
  • 3ztq, 3zto, 3ztp, 3ztr, 3zts - NDK – Aquifex aeolicus
    
  • 4dut - BtNDK – Burkholderia thailandensis
    
  • 2cwk - PhNDK – Pyrococcus horikoshii
    
  • 3vgs, 3vgt - HaNDK – Halomonas
    
  • 3vgu, 3vgv - HaNDK (mutant)
    
  • 3vvt - NDK – reconstructed archaeal ancestral
    
  • 3vvu - NDK – reconstructed bacterial ancestral
    
  • 4f36 – TbNDK – Trypanosoma brucei
    
  • 1vya – NDK – maize
    
  • 4s0m, 4w98, 4wbf, 5yih, 5yol – NDK – Acinetobacter baumannii
    
  • 5iol, 5iom - SmNDK – Schisostoma mansoni
    
  • 5u2i – NDK – Naegleria fowleri
    
  • 5v6d – NDK – Neisseria gonnorrhoeae
    
  • 5x00 – NDK – Vibrio cholerae
    
  • 6ay1 – NDK – Helicobacter pylori
    
• NDK complex with adenine derivative
  • 1ndp, 1kdn, 2bef – DdNDK + ADP
    
  • 1b4s - DdNDK (mutant) + ADP
    
  • 1bux, 1hiy - DdNDK + ADP derivative
    
  • 1nlk - MxNDK + ADP
    
  • 2hvd - hNDK + ADP
    
  • 1ucn, 2hve - hNDK (mutant) + ADP
    
  • 1zs6 - hNDK 3 + ADP
    
  • 2dxd - PhNDK + ATP analog
    
  • 2dy9, 2dya - PhNDK + ADP
    
  • 3ngt - LmNDK + AMP
    
  • 3ngu - LmNDK + ADP
    
  • 3q8u, 3q8y - SaNDK + ADP
    
  • 4dz6 - BbNDK + ADP
    
  • 1wkl - TtNDK + ADP + ATP
    
  • 4ek2 - BtNDK + AMP derivative
    
  • 4hr2 - BtNDK + ADP
    
  • 4uof, 4uoh - sNDK + ADP derivative – shrimp
    
  • 5kk8 - SmNDK + ADP
    
• NDK complex with thymidine derivative
  • 1f3f - DdNDK (mutant) + TDP derivative + TTP derivative
    
  • 1lwx - DdNDK (mutant) + azido-TDP
    
  • 1f6t - DdNDK + TDP derivative
    
  • 1mn7 - DdNDK (mutant) + TTP derivative
    
  • 1ndc - DdNDK + TDP
    
  • 3ddi - ApNDK (mutant) + TDP – Acanthamoeba polyphaga
    
  • 3em1, 3evw, 3fbc, 3fbf, 3g2x, 3evo - ApNDK (mutant) + TDP derivative
    
• NDK complex with cytosine derivative
  • 1nhk - MxNDK + CMP
    
  • 2az3 - HsNDK + CDP
    
  • 3ee3 - ApNDK + CDP
    
  • 3etm, 3gpa, 3fc9 - ApNDK (mutant) + CDP
    
  • 3evm - ApNDK (mutant) + CDP derivative
    
  • 3q89 - SaNDK + CDP
    
  • 4fkx - TbNDK + CDP
    
  • 4uog - sNDK + CDP derivative
    
• NDK complex with guanine derivative
  • 1nue , 3bbf - hNDK + GDP
    
  • 1s59 - AtNDK + GDP derivative + GTP derivative
    
  • 3bbb - hNDK B + GMP derivative + AMP derivative
    
  • 1wkk - TtNDK + GDP
    
  • 2dxe - PhNDK + GDP
    
  • 2dxf - PhNDK + GTP analog
    
  • 3gp9 - ApNDK + GDP
    
  • 3b6b - ApNDK + GDP derivative
    
  • 3fbe, 3dkd, 3ejm - ApNDK (mutant) + GDP
    
  • 3emt, 3ena - ApNDK (mutant) + GDP derivative
    
  • 3q86 - SaNDK + GTP
    

4fky - TbNDK + GTP

• NDK complex with uridine derivative
  • 1b99 - DdNDK + UDP derivative
    
  • 3eic - ApNDK + UDP
    
  • 3elh - ApNDK + UDP derivative
    
  • 3fbb, 3fcv - ApNDK (mutant) + UDP derivative
    
  • 3fcw - ApNDK (mutant) + UDP
    
  • 3q8v - SaNDK + UDP
    
  • 4f4a - TbNDK + UDP
    
• NDK other complexes
  • 1mn9, 3fkb - DdNDK (mutant) + antiviral drug
    
  • 4cp5 - DdNDK (mutant) + PMPAPP
    
  • 5ui4 - hNDK + imidazole derivative
    

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