Structure of PDB 1b99 Chain D Binding Site BS01
Receptor Information
>1b99 Chain D (length=150) Species:
44689
(Dictyostelium discoideum) [
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VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESH
YAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAP
GSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
Ligand information
Ligand ID
POP
InChI
InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
InChIKey
XPPKVPWEQAFLFU-UHFFFAOYSA-L
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
CACTVS 3.341
O[P]([O-])(=O)O[P](O)([O-])=O
ACDLabs 10.04
[O-]P(=O)(O)OP([O-])(=O)O
OpenEye OEToolkits 1.5.0
OP(=O)([O-])OP(=O)(O)[O-]
Formula
H2 O7 P2
Name
PYROPHOSPHATE 2-
ChEMBL
DrugBank
ZINC
PDB chain
1b99 Chain D Residue 460 [
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Receptor-Ligand Complex Structure
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PDB
1b99
Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.
Resolution
2.7 Å
Binding residue
(original residue number in PDB)
H59 R92 T98
Binding residue
(residue number reindexed from 1)
H54 R87 T93
Annotation score
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.
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:1b99
,
PDBe:1b99
,
PDBj:1b99
PDBsum
1b99
PubMed
10353838
UniProt
P22887
|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)
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