3GPA
Crystal structure of the Mimivirus NDK N62L mutant complexed with CDP
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 | 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 | 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 | 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 | 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 | 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 | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE CDP A 201 |
Chain | Residue |
A | LYS9 |
A | HOH141 |
A | HOH153 |
A | HOH200 |
A | MG202 |
A | HOH210 |
A | HOH349 |
A | HOH352 |
A | HIS53 |
A | TYR58 |
A | LEU62 |
A | ARG86 |
A | ARG99 |
A | ILE106 |
A | ARG107 |
A | ASN109 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG A 202 |
Chain | Residue |
A | CDP201 |
A | HOH349 |
A | HOH352 |
site_id | AC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PO4 A 138 |
Chain | Residue |
A | GLY96 |
A | ASP101 |
A | HOH154 |
C | GLY96 |
C | ASP101 |
E | GLY96 |
E | ASP101 |
site_id | AC4 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE CDP C 201 |
Chain | Residue |
C | LYS9 |
C | HIS53 |
C | TYR58 |
C | LEU62 |
C | ARG86 |
C | ARG99 |
C | ILE106 |
C | ARG107 |
C | ASN109 |
C | HOH159 |
C | HOH170 |
C | MG202 |
C | HOH342 |
C | HOH360 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG C 202 |
Chain | Residue |
C | HOH182 |
C | CDP201 |
C | HOH342 |
C | HOH360 |
site_id | AC6 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE CDP E 201 |
Chain | Residue |
E | LYS9 |
E | HIS53 |
E | TYR58 |
E | LEU62 |
E | ARG86 |
E | ARG99 |
E | ILE106 |
E | ARG107 |
E | ASN109 |
E | HOH146 |
E | HOH164 |
E | MG202 |
E | HOH343 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG E 202 |
Chain | Residue |
E | ARG86 |
E | CDP201 |
E | HOH343 |
site_id | AC8 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE CDP B 201 |
Chain | Residue |
B | LYS9 |
B | HIS53 |
B | TYR58 |
B | LEU62 |
B | ARG86 |
B | GLN89 |
B | ARG99 |
B | ILE106 |
B | ARG107 |
B | ASN109 |
B | HOH146 |
B | HOH161 |
B | MG202 |
B | HOH211 |
B | HOH354 |
site_id | AC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG B 202 |
Chain | Residue |
B | CDP201 |
B | HOH211 |
B | HOH354 |
site_id | BC1 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE CDP D 201 |
Chain | Residue |
D | LYS9 |
D | HIS53 |
D | TYR58 |
D | LEU62 |
D | ARG86 |
D | ARG99 |
D | ILE106 |
D | ARG107 |
D | ASN109 |
D | HOH166 |
D | MG202 |
D | HOH212 |
site_id | BC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG D 202 |
Chain | Residue |
D | CDP201 |
D | HOH347 |
site_id | BC3 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE CDP F 201 |
Chain | Residue |
F | ARG107 |
F | ASN109 |
F | HOH158 |
F | HOH190 |
F | MG202 |
F | HOH213 |
F | HOH357 |
F | LYS9 |
F | HIS53 |
F | TYR58 |
F | LEU62 |
F | ARG86 |
F | ARG99 |
F | ILE106 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG F 202 |
Chain | Residue |
F | ARG86 |
F | ASP115 |
F | CDP201 |
F | HOH357 |
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 | |
C | HIS112 | |
E | HIS112 | |
B | HIS112 | |
D | HIS112 | |
F | HIS112 |
site_id | SWS_FT_FI2 |
Number of Residues | 30 |
Details | BINDING: |
Chain | Residue | Details |
A | LYS9 | |
A | TYR58 | |
A | ARG86 | |
A | ARG99 | |
A | ASN109 | |
C | LYS9 | |
C | TYR58 | |
C | ARG86 | |
C | ARG99 | |
C | ASN109 | |
E | LYS9 | |
E | TYR58 | |
E | ARG86 | |
E | ARG99 | |
E | ASN109 | |
B | LYS9 | |
B | TYR58 | |
B | ARG86 | |
B | ARG99 | |
B | ASN109 | |
D | LYS9 | |
D | TYR58 | |
D | ARG86 | |
D | ARG99 | |
D | ASN109 | |
F | LYS9 | |
F | TYR58 | |
F | ARG86 | |
F | ARG99 | |
F | ASN109 |