3B6B
Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| 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 | 0009117 | biological_process | nucleotide metabolic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide 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 | 0009117 | biological_process | nucleotide metabolic process |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide 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 | 0009117 | biological_process | nucleotide metabolic process |
| C | 0016301 | molecular_function | kinase activity |
| C | 0016740 | molecular_function | transferase activity |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide 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 | 0009117 | biological_process | nucleotide metabolic process |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016740 | molecular_function | transferase activity |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0000166 | molecular_function | nucleotide 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 | 0009117 | biological_process | nucleotide metabolic process |
| E | 0016301 | molecular_function | kinase activity |
| E | 0016740 | molecular_function | transferase activity |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0000166 | molecular_function | nucleotide 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 | 0009117 | biological_process | nucleotide metabolic process |
| F | 0016301 | molecular_function | kinase activity |
| F | 0016740 | molecular_function | transferase activity |
| F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 138 |
| Chain | Residue |
| A | ARG86 |
| A | ARG99 |
| site_id | AC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG B 138 |
| Chain | Residue |
| B | HIS53 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG D 138 |
| Chain | Residue |
| D | ARG86 |
| D | ARG99 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DGI A 139 |
| Chain | Residue |
| A | ARG86 |
| A | ARG99 |
| A | ILE106 |
| A | ARG107 |
| A | ASN109 |
| A | ASP115 |
| A | HOH181 |
| A | LYS9 |
| A | HIS53 |
| A | TYR58 |
| A | ASN62 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DGI B 140 |
| Chain | Residue |
| B | LYS9 |
| B | TYR50 |
| B | HIS53 |
| B | TYR58 |
| B | ARG86 |
| B | ARG99 |
| B | ILE106 |
| B | ARG107 |
| B | ASN109 |
| B | HIS112 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DGI C 141 |
| Chain | Residue |
| C | LYS9 |
| C | TYR50 |
| C | HIS53 |
| C | TYR58 |
| C | ASN62 |
| C | ARG86 |
| C | ARG99 |
| C | ILE106 |
| C | ARG107 |
| C | ASN109 |
| C | HIS112 |
| C | HOH185 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE DGI D 142 |
| Chain | Residue |
| D | LYS9 |
| D | HIS53 |
| D | TYR58 |
| D | ASN62 |
| D | ARG86 |
| D | ARG99 |
| D | ILE106 |
| D | ARG107 |
| D | ASN109 |
| site_id | AC8 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE DGI E 143 |
| Chain | Residue |
| E | LYS9 |
| E | HIS53 |
| E | TYR58 |
| E | ASN62 |
| E | ARG86 |
| E | ARG99 |
| E | ILE106 |
| E | ARG107 |
| E | ASN109 |
| E | HOH202 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DGI F 144 |
| Chain | Residue |
| F | LYS9 |
| F | TYR50 |
| F | HIS53 |
| F | TYR58 |
| F | ASN62 |
| F | ARG86 |
| F | GLN89 |
| F | ARG99 |
| F | ILE106 |
| F | ARG107 |
| F | ASN109 |
| F | HIS112 |
Functional Information from PROSITE/UniProt
| site_id | PS00469 |
| Number of Residues | 9 |
| Details | NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NliHASDSE |
| Chain | Residue | Details |
| A | ASN109-GLU117 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10030","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 30 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | ASN109 | |
| A | LYS9 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| D | TYR50 | |
| D | LYS9 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | TYR50 | |
| E | LYS9 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | TYR50 | |
| F | LYS9 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | ASN109 | |
| B | LYS9 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | ASN109 | |
| C | LYS9 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| D | ASN109 | |
| D | LYS9 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | ASN109 | |
| E | LYS9 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | ASN109 | |
| F | LYS9 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | TYR50 | |
| A | LYS9 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | TYR50 | |
| B | LYS9 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | TYR50 | |
| C | LYS9 |
