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 |