3Q8U
Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP
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 | 0006183 | biological_process | GTP biosynthetic process |
| A | 0006228 | biological_process | UTP biosynthetic process |
| A | 0006241 | biological_process | CTP biosynthetic process |
| A | 0009117 | biological_process | nucleotide metabolic process |
| A | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016310 | biological_process | phosphorylation |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006183 | biological_process | GTP biosynthetic process |
| B | 0006228 | biological_process | UTP biosynthetic process |
| B | 0006241 | biological_process | CTP biosynthetic process |
| B | 0009117 | biological_process | nucleotide metabolic process |
| B | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016310 | biological_process | phosphorylation |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006183 | biological_process | GTP biosynthetic process |
| C | 0006228 | biological_process | UTP biosynthetic process |
| C | 0006241 | biological_process | CTP biosynthetic process |
| C | 0009117 | biological_process | nucleotide metabolic process |
| C | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| C | 0016301 | molecular_function | kinase activity |
| C | 0016310 | biological_process | phosphorylation |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006183 | biological_process | GTP biosynthetic process |
| D | 0006228 | biological_process | UTP biosynthetic process |
| D | 0006241 | biological_process | CTP biosynthetic process |
| D | 0009117 | biological_process | nucleotide metabolic process |
| D | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016310 | biological_process | phosphorylation |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0006183 | biological_process | GTP biosynthetic process |
| E | 0006228 | biological_process | UTP biosynthetic process |
| E | 0006241 | biological_process | CTP biosynthetic process |
| E | 0009117 | biological_process | nucleotide metabolic process |
| E | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| E | 0016301 | molecular_function | kinase activity |
| E | 0016310 | biological_process | phosphorylation |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| F | 0005524 | molecular_function | ATP binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0006183 | biological_process | GTP biosynthetic process |
| F | 0006228 | biological_process | UTP biosynthetic process |
| F | 0006241 | biological_process | CTP biosynthetic process |
| F | 0009117 | biological_process | nucleotide metabolic process |
| F | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| F | 0016301 | molecular_function | kinase activity |
| F | 0016310 | biological_process | phosphorylation |
| F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE ADP A 158 |
| Chain | Residue |
| A | LYS9 |
| A | MG159 |
| A | HOH160 |
| A | HOH161 |
| A | HOH162 |
| A | HOH166 |
| A | HOH204 |
| A | HOH253 |
| A | HOH295 |
| A | HIS52 |
| A | PHE57 |
| A | LEU61 |
| A | THR91 |
| A | ARG102 |
| A | VAL109 |
| A | GLY110 |
| A | ASN112 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 159 |
| Chain | Residue |
| A | ASP118 |
| A | ADP158 |
| A | HOH161 |
| A | HOH162 |
| A | HOH166 |
| site_id | AC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ADP B 158 |
| Chain | Residue |
| B | LYS9 |
| B | HIS52 |
| B | PHE57 |
| B | THR91 |
| B | ARG102 |
| B | VAL109 |
| B | ASN112 |
| B | MG159 |
| B | HOH160 |
| B | HOH164 |
| B | HOH165 |
| B | HOH179 |
| B | HOH189 |
| B | HOH194 |
| B | HOH215 |
| B | HOH411 |
| B | HOH426 |
| E | GLY54 |
| E | HOH363 |
| E | HOH364 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG B 159 |
| Chain | Residue |
| B | ASP118 |
| B | ADP158 |
| B | HOH160 |
| B | HOH165 |
| B | HOH426 |
| E | GLY54 |
| E | HOH363 |
| site_id | AC5 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE ADP C 158 |
| Chain | Residue |
| C | LYS9 |
| C | HIS52 |
| C | PHE57 |
| C | THR91 |
| C | ARG102 |
| C | VAL109 |
| C | GLY110 |
| C | ASN112 |
| C | HOH159 |
| C | HOH160 |
| C | HOH162 |
| C | HOH163 |
| C | HOH172 |
| C | HOH227 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE ADP D 158 |
| Chain | Residue |
| D | LYS9 |
| D | HIS52 |
| D | PHE57 |
| D | LEU61 |
| D | THR91 |
| D | ARG102 |
| D | VAL109 |
| D | GLY110 |
| D | ASN112 |
| D | MG159 |
| D | HOH161 |
| D | HOH162 |
| D | HOH174 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG D 159 |
| Chain | Residue |
| D | ASP118 |
| D | ADP158 |
| D | HOH160 |
| D | HOH161 |
| site_id | AC8 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE ADP E 158 |
| Chain | Residue |
| E | HOH291 |
| A | GLU149 |
| E | LYS9 |
| E | HIS52 |
| E | PHE57 |
| E | THR91 |
| E | ARG102 |
| E | VAL109 |
| E | ASN112 |
| E | MG159 |
| E | HOH160 |
| E | HOH165 |
| E | HOH166 |
| E | HOH168 |
| E | HOH169 |
| E | HOH170 |
| E | HOH173 |
| E | HOH174 |
| E | HOH207 |
| E | HOH249 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 159 |
| Chain | Residue |
| E | ASP118 |
| E | ADP158 |
| E | HOH165 |
| E | HOH169 |
| E | HOH170 |
| site_id | BC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE ADP F 158 |
| Chain | Residue |
| F | LYS9 |
| F | HIS52 |
| F | PHE57 |
| F | LEU61 |
| F | THR91 |
| F | ARG102 |
| F | VAL109 |
| F | ASN112 |
| F | MG159 |
| F | HOH427 |
| F | HOH428 |
| F | HOH429 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG F 159 |
| Chain | Residue |
| F | GLU51 |
| F | ASP118 |
| F | ADP158 |
| F | HOH428 |
| F | HOH429 |
Functional Information from PROSITE/UniProt
| site_id | PS00469 |
| Number of Residues | 9 |
| Details | NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSL |
| Chain | Residue | Details |
| A | ASN112-LEU120 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|HAMAP-Rule:MF_00451 |
| Chain | Residue | Details |
| A | HIS115 | |
| B | HIS115 | |
| C | HIS115 | |
| D | HIS115 | |
| E | HIS115 | |
| F | HIS115 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 36 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00451 |
| Chain | Residue | Details |
| A | LYS9 | |
| B | THR91 | |
| B | ARG102 | |
| B | ASN112 | |
| C | LYS9 | |
| C | PHE57 | |
| C | ARG85 | |
| C | THR91 | |
| C | ARG102 | |
| C | ASN112 | |
| D | LYS9 | |
| A | PHE57 | |
| D | PHE57 | |
| D | ARG85 | |
| D | THR91 | |
| D | ARG102 | |
| D | ASN112 | |
| E | LYS9 | |
| E | PHE57 | |
| E | ARG85 | |
| E | THR91 | |
| E | ARG102 | |
| A | ARG85 | |
| E | ASN112 | |
| F | LYS9 | |
| F | PHE57 | |
| F | ARG85 | |
| F | THR91 | |
| F | ARG102 | |
| F | ASN112 | |
| A | THR91 | |
| A | ARG102 | |
| A | ASN112 | |
| B | LYS9 | |
| B | PHE57 | |
| B | ARG85 |
