2A2Z
Crystal Structure of human deoxycytidine kinase in complex with deoxycytidine and uridine diphosphate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004136 | molecular_function | deoxyadenosine kinase activity |
| A | 0004137 | molecular_function | deoxycytidine kinase activity |
| A | 0004138 | molecular_function | deoxyguanosine kinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005829 | cellular_component | cytosol |
| A | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| A | 0006220 | biological_process | pyrimidine nucleotide metabolic process |
| A | 0008144 | molecular_function | obsolete drug binding |
| A | 0009224 | biological_process | CMP biosynthetic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0019136 | molecular_function | deoxynucleoside kinase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0043771 | molecular_function | cytidine kinase activity |
| A | 0106383 | biological_process | dAMP salvage |
| A | 1901135 | biological_process | carbohydrate derivative metabolic process |
| A | 1901293 | biological_process | nucleoside phosphate biosynthetic process |
| B | 0004136 | molecular_function | deoxyadenosine kinase activity |
| B | 0004137 | molecular_function | deoxycytidine kinase activity |
| B | 0004138 | molecular_function | deoxyguanosine kinase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005829 | cellular_component | cytosol |
| B | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| B | 0006220 | biological_process | pyrimidine nucleotide metabolic process |
| B | 0008144 | molecular_function | obsolete drug binding |
| B | 0009224 | biological_process | CMP biosynthetic process |
| B | 0016301 | molecular_function | kinase activity |
| B | 0019136 | molecular_function | deoxynucleoside kinase activity |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0043771 | molecular_function | cytidine kinase activity |
| B | 0106383 | biological_process | dAMP salvage |
| B | 1901135 | biological_process | carbohydrate derivative metabolic process |
| B | 1901293 | biological_process | nucleoside phosphate biosynthetic process |
| C | 0004136 | molecular_function | deoxyadenosine kinase activity |
| C | 0004137 | molecular_function | deoxycytidine kinase activity |
| C | 0004138 | molecular_function | deoxyguanosine kinase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005829 | cellular_component | cytosol |
| C | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| C | 0006220 | biological_process | pyrimidine nucleotide metabolic process |
| C | 0008144 | molecular_function | obsolete drug binding |
| C | 0009224 | biological_process | CMP biosynthetic process |
| C | 0016301 | molecular_function | kinase activity |
| C | 0019136 | molecular_function | deoxynucleoside kinase activity |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0043771 | molecular_function | cytidine kinase activity |
| C | 0106383 | biological_process | dAMP salvage |
| C | 1901135 | biological_process | carbohydrate derivative metabolic process |
| C | 1901293 | biological_process | nucleoside phosphate biosynthetic process |
| D | 0004136 | molecular_function | deoxyadenosine kinase activity |
| D | 0004137 | molecular_function | deoxycytidine kinase activity |
| D | 0004138 | molecular_function | deoxyguanosine kinase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005829 | cellular_component | cytosol |
| D | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| D | 0006220 | biological_process | pyrimidine nucleotide metabolic process |
| D | 0008144 | molecular_function | obsolete drug binding |
| D | 0009224 | biological_process | CMP biosynthetic process |
| D | 0016301 | molecular_function | kinase activity |
| D | 0019136 | molecular_function | deoxynucleoside kinase activity |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0043771 | molecular_function | cytidine kinase activity |
| D | 0106383 | biological_process | dAMP salvage |
| D | 1901135 | biological_process | carbohydrate derivative metabolic process |
| D | 1901293 | biological_process | nucleoside phosphate biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CA A 261 |
| Chain | Residue |
| A | ASN60 |
| C | GLU230 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CA C 261 |
| Chain | Residue |
| A | GLU230 |
| C | ASN60 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 302 |
| Chain | Residue |
| A | HOH307 |
| A | SER35 |
| A | GLU127 |
| A | UDP301 |
| A | HOH305 |
| A | HOH306 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 402 |
| Chain | Residue |
| B | SER35 |
| B | GLU127 |
| B | UDP401 |
| B | HOH405 |
| B | HOH406 |
| B | HOH407 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 502 |
| Chain | Residue |
| C | SER35 |
| C | GLU127 |
| C | UDP501 |
| C | HOH505 |
| C | HOH506 |
| C | HOH507 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 602 |
| Chain | Residue |
| D | SER35 |
| D | GLU127 |
| D | UDP601 |
| D | HOH605 |
| D | HOH606 |
| D | HOH607 |
| site_id | AC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE DCZ A 304 |
| Chain | Residue |
| A | GLU53 |
| A | TRP58 |
| A | LEU82 |
| A | MET85 |
| A | TYR86 |
| A | PHE96 |
| A | GLN97 |
| A | ARG128 |
| A | ASP133 |
| A | PHE137 |
| A | GLU197 |
| A | HOH312 |
| A | HOH319 |
| site_id | AC8 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE UDP A 301 |
| Chain | Residue |
| A | ALA31 |
| A | ALA32 |
| A | GLY33 |
| A | LYS34 |
| A | SER35 |
| A | THR36 |
| A | GLU127 |
| A | ARG188 |
| A | ARG192 |
| A | ASP241 |
| A | PHE242 |
| A | LYS243 |
| A | MG302 |
| A | HOH312 |
| site_id | AC9 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE DCZ B 404 |
| Chain | Residue |
| B | ILE30 |
| B | GLU53 |
| B | TRP58 |
| B | LEU82 |
| B | MET85 |
| B | TYR86 |
| B | PHE96 |
| B | GLN97 |
| B | ARG128 |
| B | ASP133 |
| B | PHE137 |
| B | ARG194 |
| B | GLU197 |
| B | HOH410 |
| site_id | BC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE UDP B 401 |
| Chain | Residue |
| B | ALA31 |
| B | GLY33 |
| B | LYS34 |
| B | SER35 |
| B | THR36 |
| B | GLU127 |
| B | ARG188 |
| B | LEU191 |
| B | ARG192 |
| B | ASP241 |
| B | PHE242 |
| B | LYS243 |
| B | MG402 |
| B | HOH410 |
| site_id | BC2 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DCZ C 504 |
| Chain | Residue |
| C | ILE30 |
| C | GLU53 |
| C | TYR86 |
| C | PHE96 |
| C | GLN97 |
| C | ARG128 |
| C | ASP133 |
| C | PHE137 |
| C | GLU197 |
| C | HOH507 |
| C | HOH510 |
| site_id | BC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE UDP C 501 |
| Chain | Residue |
| C | THR36 |
| C | GLU127 |
| C | ARG188 |
| C | LEU191 |
| C | ARG192 |
| C | ASP241 |
| C | PHE242 |
| C | LYS243 |
| C | MG502 |
| C | HOH514 |
| C | HOH519 |
| C | ALA31 |
| C | ALA32 |
| C | GLY33 |
| C | LYS34 |
| C | SER35 |
| site_id | BC4 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DCZ D 604 |
| Chain | Residue |
| D | ILE30 |
| D | GLU53 |
| D | TRP58 |
| D | TYR86 |
| D | PHE96 |
| D | GLN97 |
| D | ARG128 |
| D | ASP133 |
| D | PHE137 |
| D | ARG194 |
| D | GLU197 |
| D | HOH609 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE UDP D 601 |
| Chain | Residue |
| D | ALA31 |
| D | ALA32 |
| D | GLY33 |
| D | LYS34 |
| D | SER35 |
| D | THR36 |
| D | GLU127 |
| D | ARG188 |
| D | LEU191 |
| D | ARG192 |
| D | ASP241 |
| D | PHE242 |
| D | LYS243 |
| D | MG602 |
| D | HOH609 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255 |
| Chain | Residue | Details |
| A | GLU145 | |
| B | GLU145 | |
| C | GLU145 | |
| D | GLU145 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 36 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ALA31 | |
| B | ALA31 | |
| B | ALA56 | |
| B | ARG104 | |
| B | LYS115 | |
| B | CYS146 | |
| B | GLU151 | |
| B | GLU206 | |
| B | TRP215 | |
| B | SER258 | |
| C | ALA31 | |
| A | ALA56 | |
| C | ALA56 | |
| C | ARG104 | |
| C | LYS115 | |
| C | CYS146 | |
| C | GLU151 | |
| C | GLU206 | |
| C | TRP215 | |
| C | SER258 | |
| D | ALA31 | |
| D | ALA56 | |
| A | ARG104 | |
| D | ARG104 | |
| D | LYS115 | |
| D | CYS146 | |
| D | GLU151 | |
| D | GLU206 | |
| D | TRP215 | |
| D | SER258 | |
| A | LYS115 | |
| A | CYS146 | |
| A | GLU151 | |
| A | GLU206 | |
| A | TRP215 | |
| A | SER258 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine; by CK1 => ECO:0000305|PubMed:20637175 |
| Chain | Residue | Details |
| A | ALA14 | |
| A | GLY18 | |
| B | ALA14 | |
| B | GLY18 | |
| C | ALA14 | |
| C | GLY18 | |
| D | ALA14 | |
| D | GLY18 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by CK1 => ECO:0000305|PubMed:20637175 |
| Chain | Residue | Details |
| A | GLU90 | |
| B | GLU90 | |
| C | GLU90 | |
| D | GLU90 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:20637175, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | TRP92 | |
| B | TRP92 | |
| C | TRP92 | |
| D | TRP92 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2ocp |
| Chain | Residue | Details |
| A | GLU53 | |
| A | ARG128 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2ocp |
| Chain | Residue | Details |
| B | GLU53 | |
| B | ARG128 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2ocp |
| Chain | Residue | Details |
| C | GLU53 | |
| C | ARG128 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2ocp |
| Chain | Residue | Details |
| D | GLU53 | |
| D | ARG128 |
