3FKB
Structure of NDPK H122G and tenofovir-diphosphate
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 | 0016310 | biological_process | phosphorylation |
| 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 | 0016310 | biological_process | phosphorylation |
| 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 | 0016310 | biological_process | phosphorylation |
| 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 |
| D | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005840 | cellular_component | ribosome |
| D | 0005856 | cellular_component | cytoskeleton |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0006183 | biological_process | GTP biosynthetic process |
| D | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| D | 0006228 | biological_process | UTP biosynthetic process |
| D | 0006241 | biological_process | CTP biosynthetic process |
| D | 0006414 | biological_process | translational elongation |
| D | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| D | 0009117 | biological_process | nucleotide metabolic process |
| D | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| D | 0009617 | biological_process | response to bacterium |
| D | 0015629 | cellular_component | actin cytoskeleton |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016310 | biological_process | phosphorylation |
| D | 0019954 | biological_process | asexual reproduction |
| D | 0030036 | biological_process | actin cytoskeleton organization |
| D | 0030141 | cellular_component | secretory granule |
| D | 0045335 | cellular_component | phagocytic vesicle |
| D | 0045920 | biological_process | negative regulation of exocytosis |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0048550 | biological_process | negative regulation of pinocytosis |
| D | 0050765 | biological_process | negative regulation of phagocytosis |
| E | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005840 | cellular_component | ribosome |
| E | 0005856 | cellular_component | cytoskeleton |
| E | 0005886 | cellular_component | plasma membrane |
| E | 0006183 | biological_process | GTP biosynthetic process |
| E | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| E | 0006228 | biological_process | UTP biosynthetic process |
| E | 0006241 | biological_process | CTP biosynthetic process |
| E | 0006414 | biological_process | translational elongation |
| E | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| E | 0009117 | biological_process | nucleotide metabolic process |
| E | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| E | 0009617 | biological_process | response to bacterium |
| E | 0015629 | cellular_component | actin cytoskeleton |
| E | 0016301 | molecular_function | kinase activity |
| E | 0016310 | biological_process | phosphorylation |
| E | 0019954 | biological_process | asexual reproduction |
| E | 0030036 | biological_process | actin cytoskeleton organization |
| E | 0030141 | cellular_component | secretory granule |
| E | 0045335 | cellular_component | phagocytic vesicle |
| E | 0045920 | biological_process | negative regulation of exocytosis |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0048550 | biological_process | negative regulation of pinocytosis |
| E | 0050765 | biological_process | negative regulation of phagocytosis |
| F | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| F | 0005524 | molecular_function | ATP binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005840 | cellular_component | ribosome |
| F | 0005856 | cellular_component | cytoskeleton |
| F | 0005886 | cellular_component | plasma membrane |
| F | 0006183 | biological_process | GTP biosynthetic process |
| F | 0006187 | biological_process | dGTP biosynthetic process from dGDP |
| F | 0006228 | biological_process | UTP biosynthetic process |
| F | 0006241 | biological_process | CTP biosynthetic process |
| F | 0006414 | biological_process | translational elongation |
| F | 0007186 | biological_process | G protein-coupled receptor signaling pathway |
| F | 0009117 | biological_process | nucleotide metabolic process |
| F | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| F | 0009617 | biological_process | response to bacterium |
| F | 0015629 | cellular_component | actin cytoskeleton |
| F | 0016301 | molecular_function | kinase activity |
| F | 0016310 | biological_process | phosphorylation |
| F | 0019954 | biological_process | asexual reproduction |
| F | 0030036 | biological_process | actin cytoskeleton organization |
| F | 0030141 | cellular_component | secretory granule |
| F | 0045335 | cellular_component | phagocytic vesicle |
| F | 0045920 | biological_process | negative regulation of exocytosis |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0048550 | biological_process | negative regulation of pinocytosis |
| F | 0050765 | biological_process | negative regulation of phagocytosis |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE TNM A 160 |
| Chain | Residue |
| A | LYS16 |
| A | HOH1016 |
| A | HOH1017 |
| A | HOH1019 |
| A | HOH1022 |
| A | HOH1282 |
| A | HOH1335 |
| A | HOH1428 |
| A | HOH1626 |
| A | HOH1627 |
| A | HOH1861 |
| A | PHE64 |
| B | HOH1863 |
| A | LEU68 |
| A | ARG92 |
| A | THR98 |
| A | ARG109 |
| A | VAL116 |
| A | ASN119 |
| A | MG156 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 156 |
| Chain | Residue |
| A | TNM160 |
| A | HOH1016 |
| A | HOH1019 |
| A | HOH1020 |
| A | HOH1335 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 157 |
| Chain | Residue |
| A | GLU146 |
| A | LYS148 |
| A | HOH1928 |
| D | SER74 |
| D | GLY75 |
| D | PRO76 |
| site_id | AC4 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE TNM B 160 |
| Chain | Residue |
| B | LYS16 |
| B | HIS59 |
| B | PHE64 |
| B | LEU68 |
| B | ARG92 |
| B | THR98 |
| B | ARG109 |
| B | VAL116 |
| B | GLY117 |
| B | ASN119 |
| B | MG156 |
| B | HOH1011 |
| B | HOH1012 |
| B | HOH1554 |
| B | HOH1597 |
| B | HOH1814 |
| B | HOH1842 |
| B | HOH1843 |
| B | HOH1845 |
| B | HOH2040 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 156 |
| Chain | Residue |
| B | TNM160 |
| B | HOH1554 |
| B | HOH1597 |
| B | HOH1814 |
| B | HOH2040 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 157 |
| Chain | Residue |
| B | VAL38 |
| B | LYS148 |
| B | HOH1405 |
| B | HOH1505 |
| B | HOH1694 |
| B | HOH1794 |
| E | ALA21 |
| E | HOH1641 |
| site_id | AC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TNM C 160 |
| Chain | Residue |
| C | LYS16 |
| C | TYR56 |
| C | HIS59 |
| C | PHE64 |
| C | LEU68 |
| C | ARG92 |
| C | ARG109 |
| C | VAL116 |
| C | ASN119 |
| C | MG156 |
| C | HOH1013 |
| C | HOH1014 |
| C | HOH1317 |
| C | HOH1848 |
| C | HOH1849 |
| C | HOH1850 |
| C | HOH1851 |
| C | HOH2043 |
| C | HOH2158 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG C 156 |
| Chain | Residue |
| C | TNM160 |
| C | HOH1014 |
| C | HOH1849 |
| C | HOH1850 |
| C | HOH1851 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL C 157 |
| Chain | Residue |
| C | ARG92 |
| C | GLY96 |
| C | VAL97 |
| C | THR98 |
| C | HOH1623 |
| C | HOH1856 |
| C | HOH1962 |
| site_id | BC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE TNV D 160 |
| Chain | Residue |
| D | PHE64 |
| D | ARG92 |
| D | ARG109 |
| D | VAL116 |
| D | GLY117 |
| D | ASN119 |
| D | MG156 |
| D | HOH1001 |
| D | HOH1005 |
| D | HOH1327 |
| D | HOH1831 |
| D | HOH1834 |
| D | HOH2154 |
| D | LYS16 |
| D | TYR56 |
| D | GLU58 |
| D | HIS59 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG D 156 |
| Chain | Residue |
| D | TNV160 |
| D | HOH1001 |
| D | HOH1831 |
| D | HOH1834 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL D 157 |
| Chain | Residue |
| D | ASN99 |
| D | HOH2257 |
| F | HOH1599 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO D 158 |
| Chain | Residue |
| D | VAL38 |
| D | LYS148 |
| D | PRO149 |
| D | ASN150 |
| D | TYR154 |
| D | HOH1572 |
| D | HOH1961 |
| D | HOH2276 |
| site_id | BC5 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE TNM E 160 |
| Chain | Residue |
| D | HOH1868 |
| E | LYS16 |
| E | HIS59 |
| E | PHE64 |
| E | LEU68 |
| E | ARG92 |
| E | THR98 |
| E | ARG109 |
| E | VAL116 |
| E | ASN119 |
| E | MG156 |
| E | HOH1024 |
| E | HOH1025 |
| E | HOH1026 |
| E | HOH1028 |
| E | HOH1029 |
| E | HOH1032 |
| E | HOH1372 |
| E | HOH1581 |
| E | HOH1590 |
| E | HOH1864 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 156 |
| Chain | Residue |
| E | TNM160 |
| E | HOH1024 |
| E | HOH1025 |
| E | HOH1026 |
| E | HOH1029 |
| site_id | BC7 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE TNM F 160 |
| Chain | Residue |
| E | GLU155 |
| E | HOH2090 |
| F | LYS16 |
| F | PHE64 |
| F | LEU68 |
| F | ARG92 |
| F | THR98 |
| F | ARG109 |
| F | VAL116 |
| F | ASN119 |
| F | MG156 |
| F | HOH1036 |
| F | HOH1038 |
| F | HOH1043 |
| F | HOH1045 |
| F | HOH1046 |
| F | HOH1049 |
| F | HOH1050 |
| F | HOH1106 |
| F | HOH1869 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG F 156 |
| Chain | Residue |
| F | TNM160 |
| F | HOH1043 |
| F | HOH1044 |
| F | HOH1045 |
| F | HOH1046 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO F 157 |
| Chain | Residue |
| E | HOH1307 |
| F | GLY67 |
| F | SER70 |
| F | PHE71 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO F 158 |
| Chain | Residue |
| F | VAL6 |
| F | ASN7 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | ACT_SITE: Pros-phosphohistidine intermediate |
| Chain | Residue | Details |
| A | GLY122 | |
| B | GLY122 | |
| C | GLY122 | |
| D | GLY122 | |
| E | GLY122 | |
| F | GLY122 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 36 |
| 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 | |
| D | LYS16 | |
| A | PHE64 | |
| D | PHE64 | |
| D | ARG92 | |
| D | THR98 | |
| D | ARG109 | |
| D | ASN119 | |
| E | LYS16 | |
| E | PHE64 | |
| E | ARG92 | |
| E | THR98 | |
| E | ARG109 | |
| A | ARG92 | |
| E | ASN119 | |
| F | LYS16 | |
| F | PHE64 | |
| F | ARG92 | |
| F | THR98 | |
| F | ARG109 | |
| F | ASN119 | |
| 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 | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| D | TYR56 | |
| D | LYS16 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | TYR56 | |
| E | LYS16 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | TYR56 | |
| F | 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 |
| D | ASN119 | |
| D | LYS16 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | ASN119 | |
| E | LYS16 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | ASN119 | |
| F | LYS16 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | TYR56 | |
| A | LYS16 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | TYR56 | |
| B | LYS16 |
| site_id | CSA9 |
| 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 |
| site_id | MCSA4 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| D | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| D | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| D | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| D | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| D | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
| site_id | MCSA5 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| E | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| E | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| E | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| E | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| E | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
| site_id | MCSA6 |
| Number of Residues | 5 |
| Details | M-CSA 150 |
| Chain | Residue | Details |
| F | LYS16 | electrostatic stabiliser, hydrogen bond donor |
| F | TYR56 | electrostatic stabiliser, hydrogen bond donor |
| F | ASN119 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role |
| F | GLY122 | hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| F | GLU133 | hydrogen bond acceptor, increase nucleophilicity, steric role |
