3GP9
Crystal structure of the Mimivirus NDK complexed with GDP
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
A | 0016301 | molecular_function | kinase activity |
A | 0016310 | biological_process | phosphorylation |
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
B | 0016301 | molecular_function | kinase activity |
B | 0016310 | biological_process | phosphorylation |
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
C | 0016301 | molecular_function | kinase activity |
C | 0016310 | biological_process | phosphorylation |
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
D | 0016301 | molecular_function | kinase activity |
D | 0016310 | biological_process | phosphorylation |
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
E | 0016301 | molecular_function | kinase activity |
E | 0016310 | biological_process | phosphorylation |
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 | 0009142 | biological_process | nucleoside triphosphate biosynthetic process |
F | 0016301 | molecular_function | kinase activity |
F | 0016310 | biological_process | phosphorylation |
F | 0016740 | molecular_function | transferase activity |
F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GDP A 138 |
Chain | Residue |
A | LYS9 |
A | TYR50 |
A | TYR58 |
A | ARG99 |
A | ILE106 |
A | ARG107 |
A | ASN109 |
A | HIS112 |
A | MG140 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PO4 A 139 |
Chain | Residue |
A | ASN91 |
A | ILE92 |
A | ARG99 |
A | ASN109 |
A | HOH274 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 140 |
Chain | Residue |
A | GLN89 |
A | HIS112 |
A | ALA113 |
A | GDP138 |
A | HOH376 |
site_id | AC4 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE GDP B 138 |
Chain | Residue |
B | LYS9 |
B | TYR50 |
B | HIS53 |
B | TYR58 |
B | ASN62 |
B | ARG86 |
B | GLN89 |
B | ARG99 |
B | ILE106 |
B | ARG107 |
B | ASN109 |
B | HIS112 |
B | MG140 |
site_id | AC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PO4 B 139 |
Chain | Residue |
B | ASN91 |
B | ILE92 |
B | ARG99 |
B | ASP105 |
B | ASN109 |
site_id | AC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG B 140 |
Chain | Residue |
B | ARG86 |
B | GLN89 |
B | HIS112 |
B | ALA113 |
B | GDP138 |
site_id | AC7 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE GDP C 138 |
Chain | Residue |
C | LYS9 |
C | TYR50 |
C | TYR58 |
C | ARG86 |
C | GLN89 |
C | ARG99 |
C | ILE106 |
C | ARG107 |
C | HIS112 |
C | MG140 |
C | HOH648 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE PO4 C 139 |
Chain | Residue |
C | ASN91 |
C | ILE92 |
C | ARG99 |
C | ASN109 |
site_id | AC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG C 140 |
Chain | Residue |
C | ARG86 |
C | GLN89 |
C | HIS112 |
C | ALA113 |
C | GDP138 |
site_id | BC1 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GDP D 138 |
Chain | Residue |
D | LYS9 |
D | TYR50 |
D | TYR58 |
D | ARG99 |
D | ILE106 |
D | ASN109 |
D | HIS112 |
D | MG140 |
D | HOH171 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PO4 D 139 |
Chain | Residue |
D | ASN91 |
D | ILE92 |
D | ARG99 |
D | ILE106 |
D | ASN109 |
D | HOH382 |
site_id | BC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG D 140 |
Chain | Residue |
D | GLN89 |
D | ARG99 |
D | HIS112 |
D | ALA113 |
D | GDP138 |
site_id | BC4 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE GDP E 138 |
Chain | Residue |
E | LYS9 |
E | TYR50 |
E | HIS53 |
E | TYR58 |
E | ASN62 |
E | ARG86 |
E | ARG99 |
E | ILE106 |
E | ARG107 |
E | ASN109 |
E | HIS112 |
E | PO4139 |
E | MG140 |
site_id | BC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 E 139 |
Chain | Residue |
E | GDP138 |
E | HOH624 |
E | HOH644 |
E | ASN91 |
E | ILE92 |
E | ARG99 |
E | ASN109 |
site_id | BC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG E 140 |
Chain | Residue |
E | ARG86 |
E | GLN89 |
E | ARG99 |
E | HIS112 |
E | ALA113 |
E | GDP138 |
site_id | BC7 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE GDP F 138 |
Chain | Residue |
F | LYS9 |
F | TYR50 |
F | HIS53 |
F | TYR58 |
F | ARG86 |
F | GLN89 |
F | ARG99 |
F | ILE106 |
F | ARG107 |
F | ASN109 |
F | HIS112 |
F | MG140 |
F | HOH664 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PO4 F 139 |
Chain | Residue |
F | ASN91 |
F | ILE92 |
F | ARG99 |
F | ASN109 |
F | HOH380 |
F | HOH664 |
site_id | BC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG F 140 |
Chain | Residue |
F | ARG86 |
F | GLN89 |
F | HIS112 |
F | ALA113 |
F | GDP138 |
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 |