5U2I
Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0006183 | biological_process | GTP biosynthetic process |
| A | 0006228 | biological_process | UTP biosynthetic process |
| A | 0006241 | biological_process | CTP biosynthetic process |
| A | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0006183 | biological_process | GTP biosynthetic process |
| B | 0006228 | biological_process | UTP biosynthetic process |
| B | 0006241 | biological_process | CTP biosynthetic process |
| B | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| B | 0016301 | molecular_function | kinase activity |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| C | 0005524 | molecular_function | ATP binding |
| C | 0006183 | biological_process | GTP biosynthetic process |
| C | 0006228 | biological_process | UTP biosynthetic process |
| C | 0006241 | biological_process | CTP biosynthetic process |
| C | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| C | 0016301 | molecular_function | kinase activity |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| D | 0005524 | molecular_function | ATP binding |
| D | 0006183 | biological_process | GTP biosynthetic process |
| D | 0006228 | biological_process | UTP biosynthetic process |
| D | 0006241 | biological_process | CTP biosynthetic process |
| D | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| D | 0016301 | molecular_function | kinase activity |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| E | 0005524 | molecular_function | ATP binding |
| E | 0006183 | biological_process | GTP biosynthetic process |
| E | 0006228 | biological_process | UTP biosynthetic process |
| E | 0006241 | biological_process | CTP biosynthetic process |
| E | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| E | 0016301 | molecular_function | kinase activity |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| F | 0005524 | molecular_function | ATP binding |
| F | 0006183 | biological_process | GTP biosynthetic process |
| F | 0006228 | biological_process | UTP biosynthetic process |
| F | 0006241 | biological_process | CTP biosynthetic process |
| F | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
| F | 0016301 | molecular_function | kinase activity |
| F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 201 |
| Chain | Residue |
| A | ARG5 |
| A | GLU140 |
| A | HOH301 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 201 |
| Chain | Residue |
| B | ARG5 |
| B | GLU140 |
| B | MG203 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | binding site for residue EDO B 202 |
| Chain | Residue |
| B | GLU137 |
| B | LEU138 |
| B | ASN139 |
| B | HOH317 |
| B | HOH330 |
| B | HOH340 |
| B | HOH347 |
| A | ILE40 |
| A | THR41 |
| B | SER136 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue MG B 203 |
| Chain | Residue |
| B | ARG5 |
| B | LYS33 |
| B | GLU78 |
| B | EDO201 |
| B | HOH331 |
| B | HOH398 |
| B | HOH399 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 201 |
| Chain | Residue |
| C | ARG5 |
| C | LEU138 |
| C | GLU140 |
| C | HOH336 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 201 |
| Chain | Residue |
| D | ARG5 |
| D | ASN139 |
| D | GLU140 |
| D | HOH432 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue FMT D 202 |
| Chain | Residue |
| D | ALA130 |
| D | LEU131 |
| D | TRP132 |
| D | PHE133 |
| D | GLN134 |
| D | HOH301 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 203 |
| Chain | Residue |
| C | HOH394 |
| D | ASP55 |
| D | GLY56 |
| D | HOH496 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 204 |
| Chain | Residue |
| B | HOH547 |
| C | HOH364 |
| D | HOH318 |
| D | HOH330 |
| D | HOH491 |
| D | HOH531 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO D 205 |
| Chain | Residue |
| D | SER136 |
| D | LEU138 |
| D | ASN139 |
| D | HOH338 |
| D | HOH402 |
| E | ILE40 |
| E | THR41 |
| E | HOH380 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue FMT D 206 |
| Chain | Residue |
| D | ARG26 |
| D | GLN29 |
| D | HOH305 |
| D | HOH325 |
| D | HOH361 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO E 201 |
| Chain | Residue |
| E | ARG5 |
| E | ASN139 |
| E | GLU140 |
| E | HOH316 |
| E | HOH439 |
| site_id | AD4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO E 202 |
| Chain | Residue |
| E | ARG104 |
| E | HIS117 |
| E | GLY118 |
| E | FMT203 |
| E | HOH307 |
| E | HOH332 |
| E | HOH422 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue FMT E 203 |
| Chain | Residue |
| E | LYS11 |
| E | TYR51 |
| E | HIS117 |
| E | EDO202 |
| E | HOH407 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO F 201 |
| Chain | Residue |
| F | ARG5 |
| F | LEU138 |
| F | ASN139 |
| F | GLU140 |
| F | HOH330 |
| F | HOH332 |
| F | HOH409 |
| site_id | AD7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO F 202 |
| Chain | Residue |
| D | LYS147 |
| F | ASP45 |
| F | LEU46 |
| F | LEU131 |
| F | HOH302 |
| F | HOH447 |
| F | HOH460 |
| site_id | AD8 |
| Number of Residues | 9 |
| Details | binding site for residue EDO F 203 |
| Chain | Residue |
| F | HOH404 |
| C | ILE40 |
| C | THR41 |
| C | HOH451 |
| F | SER136 |
| F | LEU138 |
| F | ASN139 |
| F | HOH306 |
| F | HOH379 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO F 204 |
| Chain | Residue |
| F | ARG87 |
| F | ARG104 |
| F | HIS117 |
| F | GLY118 |
| F | HOH304 |
| F | HOH309 |
| F | HOH360 |
| F | HOH451 |
Functional Information from PROSITE/UniProt
| site_id | PS00469 |
| Number of Residues | 9 |
| Details | NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDAV |
| Chain | Residue | Details |
| A | ASN114-VAL122 |
