1NDC
X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005840 | cellular_component | ribosome |
| A | 0005856 | cellular_component | cytoskeleton |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006183 | biological_process | GTP biosynthetic process |
| A | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| A | 0006228 | biological_process | UTP biosynthetic process |
| A | 0006241 | biological_process | CTP biosynthetic process |
| A | 0006414 | biological_process | translational elongation |
| A | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| A | 0009117 | biological_process | nucleotide metabolic process |
| A | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| A | 0009617 | biological_process | response to bacterium |
| A | 0015629 | cellular_component | actin cytoskeleton |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016310 | biological_process | phosphorylation |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019954 | biological_process | asexual reproduction |
| A | 0030036 | biological_process | actin cytoskeleton organization |
| A | 0030141 | cellular_component | secretory granule |
| A | 0045335 | cellular_component | phagocytic vesicle |
| A | 0045920 | biological_process | negative regulation of exocytosis |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048550 | biological_process | negative regulation of pinocytosis |
| A | 0050765 | biological_process | negative regulation of phagocytosis |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 161 |
| Chain | Residue |
| A | TYD160 |
| A | HOH204 |
| A | HOH224 |
| A | HOH243 |
| A | HOH264 |
| site_id | AC2 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TYD A 160 |
| Chain | Residue |
| A | LEU68 |
| A | ARG92 |
| A | THR98 |
| A | ARG109 |
| A | VAL116 |
| A | ASN119 |
| A | MG161 |
| A | HOH204 |
| A | HOH224 |
| A | HOH232 |
| A | HOH243 |
| A | HOH246 |
| A | HOH264 |
| A | HOH270 |
| A | HOH284 |
| A | LYS16 |
| A | HIS59 |
| A | ARG62 |
| A | PHE64 |
Functional Information from PROSITE/UniProt
| site_id | PS00469 |
| Number of Residues | 9 |
| Details | NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSV |
| Chain | Residue | Details |
| A | ASN119-VAL127 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Pros-phosphohistidine intermediate |
| Chain | Residue | Details |
| A | HIS122 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | LYS16 | |
| A | PHE64 | |
| A | ARG92 | |
| A | THR98 | |
| A | ARG109 | |
| A | ASN119 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| A | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| A | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| A | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| A | HIS122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
