2AZ3
Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in complex 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 | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| C | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| D | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| E | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| F | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| F | 0005524 | molecular_function | ATP binding |
| F | 0005737 | cellular_component | cytoplasm |
| 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 | 0046872 | molecular_function | metal ion binding |
| G | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| G | 0005524 | molecular_function | ATP binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0006183 | biological_process | GTP biosynthetic process |
| G | 0006228 | biological_process | UTP biosynthetic process |
| G | 0006241 | biological_process | CTP biosynthetic process |
| G | 0009117 | biological_process | nucleotide metabolic process |
| G | 0016301 | molecular_function | kinase activity |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| H | 0005524 | molecular_function | ATP binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0006183 | biological_process | GTP biosynthetic process |
| H | 0006228 | biological_process | UTP biosynthetic process |
| H | 0006241 | biological_process | CTP biosynthetic process |
| H | 0009117 | biological_process | nucleotide metabolic process |
| H | 0016301 | molecular_function | kinase activity |
| H | 0046872 | molecular_function | metal ion binding |
| I | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| I | 0005524 | molecular_function | ATP binding |
| I | 0005737 | cellular_component | cytoplasm |
| I | 0006183 | biological_process | GTP biosynthetic process |
| I | 0006228 | biological_process | UTP biosynthetic process |
| I | 0006241 | biological_process | CTP biosynthetic process |
| I | 0009117 | biological_process | nucleotide metabolic process |
| I | 0016301 | molecular_function | kinase activity |
| I | 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 201 |
| Chain | Residue |
| A | GLU55 |
| A | CDP1100 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 202 |
| Chain | Residue |
| B | GLU55 |
| B | CDP1200 |
| site_id | AC3 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE CDP A 1100 |
| Chain | Residue |
| A | ARG89 |
| A | THR95 |
| A | LEU113 |
| A | GLY114 |
| A | ASN116 |
| A | HIS119 |
| A | MG201 |
| A | HOH1112 |
| A | HOH1115 |
| D | GLU55 |
| D | GLU57 |
| D | ASP58 |
| A | LYS13 |
| A | GLU55 |
| A | HIS56 |
| A | PHE61 |
| A | LEU65 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE CDP B 1200 |
| Chain | Residue |
| B | LYS13 |
| B | HIS56 |
| B | PHE61 |
| B | LEU65 |
| B | ARG89 |
| B | THR95 |
| B | LEU113 |
| B | GLY114 |
| B | ASN116 |
| B | MG202 |
| F | GLU55 |
| F | GLU57 |
| F | ASP58 |
| site_id | AC5 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE CDP C 1300 |
| Chain | Residue |
| C | LYS13 |
| C | HIS56 |
| C | PHE61 |
| C | LEU65 |
| C | ARG89 |
| C | THR95 |
| C | LEU113 |
| C | GLY114 |
| C | ASN116 |
| C | HIS119 |
| C | HOH1308 |
| E | GLU55 |
| E | GLU57 |
| E | ASP58 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE CDP D 1400 |
| Chain | Residue |
| D | LYS13 |
| D | HIS56 |
| D | PHE61 |
| D | LEU65 |
| D | ARG89 |
| D | THR95 |
| D | ARG106 |
| D | LEU113 |
| D | GLY114 |
| D | ASN116 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE CDP E 1500 |
| Chain | Residue |
| E | LYS13 |
| E | HIS56 |
| E | PHE61 |
| E | LEU65 |
| E | ARG89 |
| E | THR95 |
| E | ARG106 |
| E | LEU113 |
| E | GLY114 |
| E | ASN116 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE CDP F 1600 |
| Chain | Residue |
| F | HIS56 |
| F | PHE61 |
| F | LEU65 |
| F | ARG89 |
| F | THR95 |
| F | LEU113 |
| F | GLY114 |
| F | ASN116 |
| site_id | AC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE CDP G 1700 |
| Chain | Residue |
| G | LYS13 |
| G | TYR53 |
| G | HIS56 |
| G | PHE61 |
| G | LEU65 |
| G | ARG89 |
| G | THR95 |
| G | LEU113 |
| G | GLY114 |
| G | ASN116 |
| G | HIS119 |
| G | HOH1702 |
| site_id | BC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE CDP H 1800 |
| Chain | Residue |
| G | GLU124 |
| H | LYS13 |
| H | HIS56 |
| H | PHE61 |
| H | LEU65 |
| H | ARG89 |
| H | THR95 |
| H | LEU113 |
| H | ASN116 |
| H | HIS119 |
| H | HOH1816 |
| site_id | BC2 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE CDP I 1900 |
| Chain | Residue |
| I | LYS13 |
| I | HIS56 |
| I | PHE61 |
| I | LEU65 |
| I | ARG89 |
| I | THR95 |
| I | ARG106 |
| I | LEU113 |
| I | GLY114 |
| I | ASN116 |
| I | HIS119 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 9 |
| Details | ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|HAMAP-Rule:MF_00451 |
| Chain | Residue | Details |
| A | HIS119 | |
| B | HIS119 | |
| C | HIS119 | |
| D | HIS119 | |
| E | HIS119 | |
| F | HIS119 | |
| G | HIS119 | |
| H | HIS119 | |
| I | HIS119 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 54 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000305|PubMed:16293253 |
| Chain | Residue | Details |
| A | LYS13 | |
| B | THR95 | |
| B | ARG106 | |
| B | ASN116 | |
| C | LYS13 | |
| C | PHE61 | |
| C | ARG89 | |
| C | THR95 | |
| C | ARG106 | |
| C | ASN116 | |
| D | LYS13 | |
| A | PHE61 | |
| D | PHE61 | |
| D | ARG89 | |
| D | THR95 | |
| D | ARG106 | |
| D | ASN116 | |
| E | LYS13 | |
| E | PHE61 | |
| E | ARG89 | |
| E | THR95 | |
| E | ARG106 | |
| A | ARG89 | |
| E | ASN116 | |
| F | LYS13 | |
| F | PHE61 | |
| F | ARG89 | |
| F | THR95 | |
| F | ARG106 | |
| F | ASN116 | |
| G | LYS13 | |
| G | PHE61 | |
| G | ARG89 | |
| A | THR95 | |
| G | THR95 | |
| G | ARG106 | |
| G | ASN116 | |
| H | LYS13 | |
| H | PHE61 | |
| H | ARG89 | |
| H | THR95 | |
| H | ARG106 | |
| H | ASN116 | |
| I | LYS13 | |
| A | ARG106 | |
| I | PHE61 | |
| I | ARG89 | |
| I | THR95 | |
| I | ARG106 | |
| I | ASN116 | |
| A | ASN116 | |
| B | LYS13 | |
| B | PHE61 | |
| B | ARG89 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | LYS13 | |
| A | ASN116 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| A | LYS13 | |
| A | TYR53 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | LYS13 | |
| B | TYR53 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | LYS13 | |
| C | TYR53 |
| site_id | CSA13 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| D | LYS13 | |
| D | TYR53 |
| site_id | CSA14 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | LYS13 | |
| E | TYR53 |
| site_id | CSA15 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | LYS13 | |
| F | TYR53 |
| site_id | CSA16 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| G | LYS13 | |
| G | TYR53 |
| site_id | CSA17 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| H | LYS13 | |
| H | TYR53 |
| site_id | CSA18 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| I | LYS13 | |
| I | TYR53 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| B | LYS13 | |
| B | ASN116 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| C | LYS13 | |
| C | ASN116 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| D | LYS13 | |
| D | ASN116 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| E | LYS13 | |
| E | ASN116 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| F | LYS13 | |
| F | ASN116 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| G | LYS13 | |
| G | ASN116 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| H | LYS13 | |
| H | ASN116 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1nsp |
| Chain | Residue | Details |
| I | LYS13 | |
| I | ASN116 |
