Structure of PDB 1ndp Chain A

Receptor sequence
>1ndpA (length=150) Species: 44689 (Dictyostelium discoideum) [Search protein sequence]
VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESH
YAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAP
GSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
3D structure
PDB1ndp Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase.
ChainA
Resolution2.2 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K16 Y56 N119 H122 E133
Catalytic site (residue number reindexed from 1) K11 Y51 N114 H117 E128
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ADP A H59 F64 L68 R92 T98 R109 V116 N119 H54 F59 L63 R87 T93 R104 V111 N114
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006187 dGTP biosynthetic process from dGDP
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006414 translational elongation
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0016310 phosphorylation
GO:0019954 asexual reproduction
GO:0030036 actin cytoskeleton organization
GO:0045920 negative regulation of exocytosis
GO:0048550 negative regulation of pinocytosis
GO:0050765 negative regulation of phagocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0015629 actin cytoskeleton
GO:0030141 secretory granule
GO:0045335 phagocytic vesicle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ndp, PDBe:1ndp, PDBj:1ndp
PDBsum1ndp
PubMed8286376
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

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