1B4S
STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| 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 | 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 |
| B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005840 | cellular_component | ribosome |
| B | 0005856 | cellular_component | cytoskeleton |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006183 | biological_process | GTP biosynthetic process |
| B | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| B | 0006228 | biological_process | UTP biosynthetic process |
| B | 0006241 | biological_process | CTP biosynthetic process |
| B | 0006414 | biological_process | translational elongation |
| B | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| B | 0009117 | biological_process | nucleotide metabolic process |
| B | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| B | 0009617 | biological_process | response to bacterium |
| B | 0015629 | cellular_component | actin cytoskeleton |
| B | 0016301 | molecular_function | kinase activity |
| B | 0019954 | biological_process | asexual reproduction |
| B | 0030036 | biological_process | actin cytoskeleton organization |
| B | 0030141 | cellular_component | secretory granule |
| B | 0045335 | cellular_component | phagocytic vesicle |
| B | 0045920 | biological_process | negative regulation of exocytosis |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048550 | biological_process | negative regulation of pinocytosis |
| B | 0050765 | biological_process | negative regulation of phagocytosis |
| C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005840 | cellular_component | ribosome |
| C | 0005856 | cellular_component | cytoskeleton |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0006183 | biological_process | GTP biosynthetic process |
| C | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| C | 0006228 | biological_process | UTP biosynthetic process |
| C | 0006241 | biological_process | CTP biosynthetic process |
| C | 0006414 | biological_process | translational elongation |
| C | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| C | 0009117 | biological_process | nucleotide metabolic process |
| C | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| C | 0009617 | biological_process | response to bacterium |
| C | 0015629 | cellular_component | actin cytoskeleton |
| C | 0016301 | molecular_function | kinase activity |
| C | 0019954 | biological_process | asexual reproduction |
| C | 0030036 | biological_process | actin cytoskeleton organization |
| C | 0030141 | cellular_component | secretory granule |
| C | 0045335 | cellular_component | phagocytic vesicle |
| C | 0045920 | biological_process | negative regulation of exocytosis |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0048550 | biological_process | negative regulation of pinocytosis |
| C | 0050765 | biological_process | negative regulation of phagocytosis |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PO4 A 161 |
| Chain | Residue |
| A | LYS16 |
| A | HIS55 |
| A | TYR56 |
| A | ARG92 |
| A | ARG109 |
| A | GLY122 |
| A | GLY123 |
| A | ADP160 |
| A | MG162 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 162 |
| Chain | Residue |
| A | ADP160 |
| A | PO4161 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PO4 B 161 |
| Chain | Residue |
| B | LYS16 |
| B | HIS55 |
| B | TYR56 |
| B | ARG92 |
| B | GLY122 |
| B | GLY123 |
| B | ADP160 |
| B | MG162 |
| B | HOH182 |
| B | HOH203 |
| B | HOH205 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 162 |
| Chain | Residue |
| B | ADP160 |
| B | PO4161 |
| B | HOH203 |
| B | HOH204 |
| B | HOH205 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PO4 C 161 |
| Chain | Residue |
| C | LYS16 |
| C | HIS55 |
| C | TYR56 |
| C | ARG92 |
| C | GLY122 |
| C | GLY123 |
| C | ADP160 |
| C | MG162 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG C 162 |
| Chain | Residue |
| C | ADP160 |
| C | PO4161 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE ADP A 160 |
| Chain | Residue |
| A | LYS16 |
| A | TYR56 |
| A | HIS59 |
| A | PHE64 |
| A | LEU68 |
| A | ARG92 |
| A | THR98 |
| A | ARG109 |
| A | VAL116 |
| A | ASN119 |
| A | PO4161 |
| A | MG162 |
| site_id | AC8 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE ADP B 160 |
| Chain | Residue |
| B | LYS16 |
| B | TYR56 |
| B | HIS59 |
| B | PHE64 |
| B | LEU68 |
| B | ARG92 |
| B | THR98 |
| B | ARG109 |
| B | VAL116 |
| B | ASN119 |
| B | PO4161 |
| B | MG162 |
| B | HOH175 |
| B | HOH204 |
| B | HOH205 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE ADP C 160 |
| Chain | Residue |
| C | LYS16 |
| C | TYR56 |
| C | HIS59 |
| C | ARG62 |
| C | PHE64 |
| C | LEU68 |
| C | ARG92 |
| C | THR98 |
| C | ARG109 |
| C | VAL116 |
| C | ASN119 |
| C | PO4161 |
| C | MG162 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 3 |
| Details | ACT_SITE: Pros-phosphohistidine intermediate |
| Chain | Residue | Details |
| A | GLY122 | |
| B | GLY122 | |
| C | GLY122 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | LYS16 | |
| B | THR98 | |
| B | ARG109 | |
| B | ASN119 | |
| C | LYS16 | |
| C | PHE64 | |
| C | ARG92 | |
| C | THR98 | |
| C | ARG109 | |
| C | ASN119 | |
| A | PHE64 | |
| A | ARG92 | |
| A | THR98 | |
| A | ARG109 | |
| A | ASN119 | |
| B | LYS16 | |
| B | PHE64 | |
| B | ARG92 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | ASN119 | |
| A | LYS16 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | ASN119 | |
| B | LYS16 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | ASN119 | |
| C | LYS16 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | TYR56 | |
| A | LYS16 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | TYR56 | |
| B | LYS16 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | TYR56 | |
| C | LYS16 |
| 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 | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
| site_id | MCSA2 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| B | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| B | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| B | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| B | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
| site_id | MCSA3 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| C | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| C | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| C | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| C | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| C | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
