Structure of PDB 2bef Chain B

Receptor sequence
>2befB (length=150) Species: 44689 (Dictyostelium discoideum) [Search protein sequence]
VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESH
YAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAP
GSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
3D structure
PDB2bef AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
ChainB
Resolution2.3 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 BEF B K16 Y56 R92 R109 H122 K11 Y51 R87 R104 H117
BS02 ADP B K16 H59 F64 L68 R92 T98 R109 V116 N119 K11 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2bef, PDBe:2bef, PDBj:2bef
PDBsum2bef
PubMed9108019
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

[Back to BioLiP]