4ERM
Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex at 4 Angstroms resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| A | 0006457 | biological_process | protein folding |
| A | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| A | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| A | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| A | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0044183 | molecular_function | protein folding chaperone |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005829 | cellular_component | cytosol |
| B | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| B | 0006457 | biological_process | protein folding |
| B | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| B | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| B | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| B | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0044183 | molecular_function | protein folding chaperone |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| C | 0005515 | molecular_function | protein binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005829 | cellular_component | cytosol |
| C | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| C | 0006457 | biological_process | protein folding |
| C | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| C | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| C | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| C | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0044183 | molecular_function | protein folding chaperone |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| D | 0005515 | molecular_function | protein binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005829 | cellular_component | cytosol |
| D | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| D | 0006457 | biological_process | protein folding |
| D | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| D | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| D | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| D | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0044183 | molecular_function | protein folding chaperone |
| E | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| E | 0005506 | molecular_function | iron ion binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| E | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| E | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| E | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| E | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0042802 | molecular_function | identical protein binding |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| F | 0005506 | molecular_function | iron ion binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0005829 | cellular_component | cytosol |
| F | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| F | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| F | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| F | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| F | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0042802 | molecular_function | identical protein binding |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| G | 0005506 | molecular_function | iron ion binding |
| G | 0005515 | molecular_function | protein binding |
| G | 0005737 | cellular_component | cytoplasm |
| G | 0005829 | cellular_component | cytosol |
| G | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| G | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| G | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| G | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| G | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0042802 | molecular_function | identical protein binding |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0004748 | molecular_function | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| H | 0005506 | molecular_function | iron ion binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0005737 | cellular_component | cytoplasm |
| H | 0005829 | cellular_component | cytosol |
| H | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| H | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| H | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| H | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| H | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0042802 | molecular_function | identical protein binding |
| H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE DTP A 801 |
| Chain | Residue |
| A | VAL7 |
| A | THR55 |
| A | HIS59 |
| A | ILE62 |
| A | PHE87 |
| A | LYS9 |
| A | ARG10 |
| A | GLU15 |
| A | ARG16 |
| A | ILE17 |
| A | ASN18 |
| A | LYS21 |
| A | VAL25 |
| site_id | AC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DAT A 802 |
| Chain | Residue |
| A | PRO208 |
| A | THR209 |
| A | CYS225 |
| A | ASN437 |
| A | LEU438 |
| A | CYS439 |
| A | GLU441 |
| A | LEU464 |
| A | PRO621 |
| A | SER622 |
| A | THR624 |
| A | SER625 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DTP A 803 |
| Chain | Residue |
| A | ASP232 |
| A | SER233 |
| A | LEU234 |
| A | ARG262 |
| A | ILE268 |
| A | ARG269 |
| A | HIS275 |
| A | THR276 |
| A | MG804 |
| B | SER249 |
| B | CYS292 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG A 804 |
| Chain | Residue |
| A | DTP803 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE DTP B 801 |
| Chain | Residue |
| B | VAL7 |
| B | LYS9 |
| B | ARG10 |
| B | GLU15 |
| B | ARG16 |
| B | ILE17 |
| B | ASN18 |
| B | LYS21 |
| B | ILE22 |
| B | THR55 |
| B | HIS59 |
| B | PHE87 |
| B | LYS91 |
| site_id | AC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE DAT B 802 |
| Chain | Residue |
| B | PRO208 |
| B | THR209 |
| B | CYS225 |
| B | ARG251 |
| B | GLY253 |
| B | ASN437 |
| B | CYS439 |
| B | GLU441 |
| B | LEU464 |
| B | MET620 |
| B | PRO621 |
| B | SER622 |
| B | GLU623 |
| B | THR624 |
| B | SER625 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DTP B 803 |
| Chain | Residue |
| A | SER249 |
| A | CYS292 |
| B | ASP232 |
| B | SER233 |
| B | LEU234 |
| B | ARG262 |
| B | ILE268 |
| B | ARG269 |
| B | HIS275 |
| B | THR276 |
| B | MG804 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG B 804 |
| Chain | Residue |
| B | DTP803 |
| site_id | AC9 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DTP C 801 |
| Chain | Residue |
| C | LYS9 |
| C | ARG10 |
| C | GLU15 |
| C | ARG16 |
| C | ILE17 |
| C | ASN18 |
| C | LYS21 |
| C | ILE22 |
| C | VAL25 |
| C | THR55 |
| C | HIS59 |
| site_id | BC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE DAT C 802 |
| Chain | Residue |
| C | SER622 |
| C | THR624 |
| C | SER625 |
| C | PRO208 |
| C | THR209 |
| C | SER224 |
| C | CYS225 |
| C | ASN437 |
| C | LEU438 |
| C | CYS439 |
| C | GLU441 |
| C | LEU464 |
| C | MET620 |
| C | PRO621 |
| site_id | BC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE DTP C 803 |
| Chain | Residue |
| C | ASP232 |
| C | SER233 |
| C | LEU234 |
| C | ILE237 |
| C | ARG262 |
| C | ILE268 |
| C | ARG269 |
| C | HIS275 |
| C | THR276 |
| C | MG804 |
| D | SER249 |
| D | CYS292 |
| site_id | BC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG C 804 |
| Chain | Residue |
| C | DTP803 |
| site_id | BC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE DTP D 801 |
| Chain | Residue |
| D | VAL7 |
| D | LYS9 |
| D | ARG10 |
| D | GLU15 |
| D | ARG16 |
| D | ILE17 |
| D | ASN18 |
| D | LYS21 |
| D | ILE22 |
| D | VAL25 |
| D | THR55 |
| D | HIS59 |
| D | PHE87 |
| site_id | BC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE DAT D 802 |
| Chain | Residue |
| D | PRO208 |
| D | THR209 |
| D | CYS225 |
| D | LEU438 |
| D | CYS439 |
| D | PRO621 |
| D | SER622 |
| D | THR624 |
| D | SER625 |
| site_id | BC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE DTP D 803 |
| Chain | Residue |
| C | SER249 |
| C | CYS292 |
| D | ASP232 |
| D | SER233 |
| D | LEU234 |
| D | ARG262 |
| D | ILE268 |
| D | ARG269 |
| D | HIS275 |
| D | THR276 |
| D | MG804 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG D 804 |
| Chain | Residue |
| D | ASP232 |
| D | DTP803 |
| site_id | BC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FEO E 501 |
| Chain | Residue |
| E | ASP84 |
| E | GLU115 |
| E | HIS118 |
| E | GLU204 |
| E | GLU238 |
| E | HIS241 |
| E | HOH601 |
| E | HOH602 |
| site_id | BC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FEO F 501 |
| Chain | Residue |
| F | ASP84 |
| F | GLU115 |
| F | HIS118 |
| F | GLU204 |
| F | GLU238 |
| F | HIS241 |
| F | HOH601 |
| F | HOH602 |
| site_id | CC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FEO G 501 |
| Chain | Residue |
| G | ASP84 |
| G | GLU115 |
| G | HIS118 |
| G | GLU204 |
| G | GLU238 |
| G | HIS241 |
| G | HOH601 |
| G | HOH602 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FEO H 501 |
| Chain | Residue |
| H | ASP84 |
| H | GLU115 |
| H | HIS118 |
| H | GLU204 |
| H | GLU238 |
| H | HIS241 |
| H | HOH601 |
| H | HOH602 |
Functional Information from PROSITE/UniProt
| site_id | PS00089 |
| Number of Residues | 23 |
| Details | RIBORED_LARGE Ribonucleotide reductase large subunit signature. WeaLresikthGLRNstlSAlmP |
| Chain | Residue | Details |
| A | TRP599-PRO621 |
| site_id | PS00368 |
| Number of Residues | 17 |
| Details | RIBORED_SMALL Ribonucleotide reductase small subunit signature. SEt.IHSrSYthIirnIV |
| Chain | Residue | Details |
| E | SER114-VAL130 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 270 |
| Details | Domain: {"description":"ATP-cone","evidences":[{"source":"PROSITE-ProRule","id":"PRU00492","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Proton acceptor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Cysteine radical intermediate"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 36 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9309223","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3R1R","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 36 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9309223","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4R1R","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Site: {"description":"Important for hydrogen atom transfer"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | Site: {"description":"Important for electron transfer"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | Active site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 24 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 918 |
| Chain | Residue | Details |
| E | TYR122 | pi-pi interaction, single electron relay |
| E | ASP237 | |
| A | CYS439 | hydrogen radical acceptor, hydrogen radical donor, single electron acceptor |
| A | GLU441 | proton acceptor |
| A | CYS462 | |
| A | TYR730 | pi-pi interaction, single electron relay |
| A | TYR731 | pi-pi interaction, single electron relay |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 918 |
| Chain | Residue | Details |
| F | TYR122 | pi-pi interaction, single electron relay |
| F | ASP237 | |
| B | CYS439 | hydrogen radical acceptor, hydrogen radical donor, single electron acceptor |
| B | GLU441 | proton acceptor |
| B | CYS462 | |
| B | TYR730 | pi-pi interaction, single electron relay |
| B | TYR731 | pi-pi interaction, single electron relay |
| site_id | MCSA3 |
| Number of Residues | 2 |
| Details | M-CSA 918 |
| Chain | Residue | Details |
| G | TYR122 | pi-pi interaction, single electron relay |
| G | ASP237 | |
| C | CYS439 | hydrogen radical acceptor, hydrogen radical donor, single electron acceptor |
| C | GLU441 | proton acceptor |
| C | CYS462 | |
| C | TYR730 | pi-pi interaction, single electron relay |
| C | TYR731 | pi-pi interaction, single electron relay |
| site_id | MCSA4 |
| Number of Residues | 2 |
| Details | M-CSA 918 |
| Chain | Residue | Details |
| H | TYR122 | pi-pi interaction, single electron relay |
| H | ASP237 | |
| D | CYS439 | hydrogen radical acceptor, hydrogen radical donor, single electron acceptor |
| D | GLU441 | proton acceptor |
| D | CYS462 | |
| D | TYR730 | pi-pi interaction, single electron relay |
| D | TYR731 | pi-pi interaction, single electron relay |
