3ELH
X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dUDP
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 | 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 | 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 | 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 | 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 | 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 | 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 | 11 |
Details | BINDING SITE FOR RESIDUE DUD A 160 |
Chain | Residue |
A | LYS9 |
A | ASN109 |
A | MG161 |
A | HIS53 |
A | TYR58 |
A | ASN62 |
A | ARG86 |
A | GLN89 |
A | ARG99 |
A | ILE106 |
A | ARG107 |
site_id | AC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG A 161 |
Chain | Residue |
A | ARG86 |
A | DUD160 |
site_id | AC3 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE DUD B 161 |
Chain | Residue |
B | LYS9 |
B | HIS53 |
B | TYR58 |
B | ASN62 |
B | ARG86 |
B | ARG99 |
B | ILE106 |
B | ARG107 |
B | ASN109 |
B | MG162 |
B | HOH170 |
site_id | AC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MG B 162 |
Chain | Residue |
B | DUD161 |
site_id | AC5 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE DUD C 162 |
Chain | Residue |
C | LYS9 |
C | TYR50 |
C | HIS53 |
C | TYR58 |
C | ASN62 |
C | ARG86 |
C | ARG99 |
C | ILE106 |
C | ARG107 |
C | ASN109 |
C | MG163 |
C | HOH191 |
site_id | AC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG C 163 |
Chain | Residue |
C | ARG86 |
C | DUD162 |
site_id | AC7 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE DUD D 163 |
Chain | Residue |
D | LYS9 |
D | TYR50 |
D | HIS53 |
D | TYR58 |
D | ASN62 |
D | ARG86 |
D | GLN89 |
D | ARG99 |
D | ILE106 |
D | ARG107 |
D | ASN109 |
D | MG164 |
site_id | AC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG D 164 |
Chain | Residue |
D | ASP115 |
D | DUD163 |
site_id | AC9 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE DUD E 164 |
Chain | Residue |
E | LYS9 |
E | TYR50 |
E | HIS53 |
E | TYR58 |
E | ASN62 |
E | ARG86 |
E | ARG99 |
E | ILE106 |
E | ARG107 |
E | ASN109 |
E | MG165 |
site_id | BC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG E 165 |
Chain | Residue |
E | ARG86 |
E | DUD164 |
site_id | BC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE DUD F 165 |
Chain | Residue |
F | LYS9 |
F | HIS53 |
F | TYR58 |
F | ASN62 |
F | ARG86 |
F | ARG99 |
F | ILE106 |
F | ARG107 |
F | ASN109 |
F | MG166 |
site_id | BC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG F 166 |
Chain | Residue |
F | ARG86 |
F | DUD165 |
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 | ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|PROSITE-ProRule:PRU10030 |
Chain | Residue | Details |
A | HIS112 | |
B | HIS112 | |
C | HIS112 | |
D | HIS112 | |
E | HIS112 | |
F | HIS112 |
site_id | SWS_FT_FI2 |
Number of Residues | 30 |
Details | BINDING: |
Chain | Residue | Details |
A | LYS9 | |
B | ASN109 | |
C | LYS9 | |
C | TYR58 | |
C | ARG86 | |
C | ARG99 | |
C | ASN109 | |
D | LYS9 | |
D | TYR58 | |
D | ARG86 | |
D | ARG99 | |
A | TYR58 | |
D | ASN109 | |
E | LYS9 | |
E | TYR58 | |
E | ARG86 | |
E | ARG99 | |
E | ASN109 | |
F | LYS9 | |
F | TYR58 | |
F | ARG86 | |
F | ARG99 | |
A | ARG86 | |
F | ASN109 | |
A | ARG99 | |
A | ASN109 | |
B | LYS9 | |
B | TYR58 | |
B | ARG86 | |
B | ARG99 |
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 |