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 |