5CNT
Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to UDP and dATP at 3.25 Angstroms resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| 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 | 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 | 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 | 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 | 18 |
| Details | binding site for residue UDP A 801 |
| Chain | Residue |
| A | THR209 |
| A | GLU441 |
| A | LEU464 |
| A | MET620 |
| A | PRO621 |
| A | SER622 |
| A | GLU623 |
| A | THR624 |
| A | SER625 |
| A | HOH903 |
| A | SER224 |
| A | CYS225 |
| A | GLY253 |
| A | GLN294 |
| A | ARG298 |
| A | ASN437 |
| A | LEU438 |
| A | CYS439 |
| site_id | AC2 |
| Number of Residues | 16 |
| Details | binding site for residue DTP A 802 |
| Chain | Residue |
| A | VAL7 |
| A | LYS9 |
| A | ARG10 |
| A | GLU15 |
| A | ARG16 |
| A | ILE17 |
| A | ASN18 |
| A | LYS21 |
| A | VAL25 |
| A | THR55 |
| A | HIS59 |
| A | PHE87 |
| A | LYS91 |
| A | GLY95 |
| A | MG803 |
| A | DTP804 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue MG A 803 |
| Chain | Residue |
| A | DTP802 |
| A | DTP804 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue DTP A 804 |
| Chain | Residue |
| A | LYS9 |
| A | LYS21 |
| A | VAL25 |
| A | TRP28 |
| A | DTP802 |
| A | MG803 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | binding site for residue DTP A 805 |
| Chain | Residue |
| A | ASP232 |
| A | SER233 |
| A | LEU234 |
| A | ARG262 |
| A | ILE268 |
| A | ARG269 |
| A | HIS275 |
| A | THR276 |
| A | PHE281 |
| A | MG806 |
| A | HOH909 |
| A | HOH910 |
| A | HOH911 |
| B | SER249 |
| B | CYS292 |
| B | SER293 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 806 |
| Chain | Residue |
| A | DTP805 |
| A | HOH909 |
| A | HOH910 |
| A | HOH911 |
| site_id | AC7 |
| Number of Residues | 18 |
| Details | binding site for residue UDP B 801 |
| Chain | Residue |
| B | PRO208 |
| B | THR209 |
| B | SER224 |
| B | CYS225 |
| B | GLY253 |
| B | GLN294 |
| B | ARG298 |
| B | ASN437 |
| B | LEU438 |
| B | CYS439 |
| B | GLU441 |
| B | MET620 |
| B | PRO621 |
| B | SER622 |
| B | GLU623 |
| B | THR624 |
| B | SER625 |
| B | HOH903 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | binding site for residue DTP B 802 |
| Chain | Residue |
| B | VAL7 |
| B | LYS9 |
| B | ARG10 |
| B | GLU15 |
| B | ARG16 |
| B | ILE17 |
| B | ASN18 |
| B | LYS21 |
| B | ILE22 |
| B | VAL25 |
| B | THR55 |
| B | HIS59 |
| B | ILE62 |
| B | PHE87 |
| B | LYS91 |
| B | MG803 |
| B | DTP804 |
| B | HOH908 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue MG B 803 |
| Chain | Residue |
| B | DTP804 |
| B | DTP802 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue DTP B 804 |
| Chain | Residue |
| B | LYS9 |
| B | LYS21 |
| B | VAL25 |
| B | TRP28 |
| B | PHE87 |
| B | PHE97 |
| B | DTP802 |
| B | MG803 |
| site_id | AD2 |
| Number of Residues | 15 |
| Details | binding site for residue DTP B 805 |
| Chain | Residue |
| A | SER249 |
| A | CYS292 |
| A | SER293 |
| B | ASP232 |
| B | SER233 |
| B | LEU234 |
| B | ARG262 |
| B | ILE268 |
| B | ARG269 |
| B | HIS275 |
| B | THR276 |
| B | MG806 |
| B | HOH906 |
| B | HOH909 |
| B | HOH910 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue MG B 806 |
| Chain | Residue |
| B | DTP805 |
| B | HOH906 |
| B | HOH909 |
| B | HOH910 |
| site_id | AD4 |
| Number of Residues | 18 |
| Details | binding site for residue UDP C 801 |
| Chain | Residue |
| C | THR209 |
| C | SER224 |
| C | CYS225 |
| C | GLY253 |
| C | GLN294 |
| C | ARG298 |
| C | ASN437 |
| C | LEU438 |
| C | CYS439 |
| C | GLU441 |
| C | LEU464 |
| C | MET620 |
| C | PRO621 |
| C | SER622 |
| C | GLU623 |
| C | THR624 |
| C | SER625 |
| C | HOH901 |
| site_id | AD5 |
| Number of Residues | 16 |
| Details | binding site for residue DTP C 802 |
| Chain | Residue |
| C | VAL7 |
| C | LYS9 |
| C | ARG10 |
| C | GLU15 |
| C | ARG16 |
| C | ILE17 |
| C | ASN18 |
| C | LYS21 |
| C | ILE22 |
| C | VAL25 |
| C | THR55 |
| C | HIS59 |
| C | PHE87 |
| C | LYS91 |
| C | MG803 |
| C | DTP804 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue MG C 803 |
| Chain | Residue |
| C | DTP802 |
| C | DTP804 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue DTP C 804 |
| Chain | Residue |
| C | LYS9 |
| C | LYS21 |
| C | ARG24 |
| C | VAL25 |
| C | TRP28 |
| C | PHE97 |
| C | DTP802 |
| C | MG803 |
| site_id | AD8 |
| Number of Residues | 17 |
| Details | binding site for residue DTP C 805 |
| Chain | Residue |
| C | ASP232 |
| C | SER233 |
| C | LEU234 |
| C | ILE261 |
| C | ARG262 |
| C | ILE268 |
| C | ARG269 |
| C | HIS275 |
| C | THR276 |
| C | PHE281 |
| C | MG806 |
| C | HOH902 |
| C | HOH903 |
| C | HOH904 |
| D | SER249 |
| D | CYS292 |
| D | SER293 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue MG C 806 |
| Chain | Residue |
| C | DTP805 |
| C | HOH902 |
| C | HOH903 |
| C | HOH904 |
| site_id | AE1 |
| Number of Residues | 19 |
| Details | binding site for residue UDP D 801 |
| Chain | Residue |
| D | PRO208 |
| D | THR209 |
| D | SER224 |
| D | CYS225 |
| D | GLY253 |
| D | GLN294 |
| D | ARG298 |
| D | ASN437 |
| D | LEU438 |
| D | CYS439 |
| D | GLU441 |
| D | LEU464 |
| D | MET620 |
| D | PRO621 |
| D | SER622 |
| D | GLU623 |
| D | THR624 |
| D | SER625 |
| D | HOH901 |
| site_id | AE2 |
| Number of Residues | 16 |
| Details | binding site for residue DTP D 802 |
| Chain | Residue |
| D | VAL7 |
| D | LYS9 |
| D | ARG10 |
| D | GLU15 |
| D | ARG16 |
| D | ILE17 |
| D | ASN18 |
| D | LYS21 |
| D | VAL25 |
| D | THR55 |
| D | HIS59 |
| D | PHE87 |
| D | LYS91 |
| D | GLY95 |
| D | MG803 |
| D | DTP804 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue MG D 803 |
| Chain | Residue |
| D | DTP802 |
| D | DTP804 |
| site_id | AE4 |
| Number of Residues | 7 |
| Details | binding site for residue DTP D 804 |
| Chain | Residue |
| D | LYS9 |
| D | LYS21 |
| D | VAL25 |
| D | TRP28 |
| D | PHE97 |
| D | DTP802 |
| D | MG803 |
| site_id | AE5 |
| Number of Residues | 15 |
| Details | binding site for residue DTP D 805 |
| Chain | Residue |
| C | SER249 |
| C | CYS292 |
| C | SER293 |
| D | ASP232 |
| D | SER233 |
| D | LEU234 |
| D | ARG262 |
| D | ILE268 |
| D | ARG269 |
| D | HIS275 |
| D | THR276 |
| D | MG806 |
| D | HOH903 |
| D | HOH904 |
| D | HOH905 |
| site_id | AE6 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 806 |
| Chain | Residue |
| D | DTP805 |
| D | HOH903 |
| D | HOH904 |
| D | HOH905 |
| site_id | AE7 |
| 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 | AE8 |
| 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 | AE9 |
| 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 | HOH603 |
| site_id | AF1 |
| 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 | HOH602 |
| H | HOH603 |
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 | 4 |
| Details | ACT_SITE: |
| Chain | Residue | Details |
| E | TYR122 | |
| F | TYR122 | |
| G | TYR122 | |
| H | TYR122 | |
| C | ASN437 | |
| C | GLU441 | |
| D | ASN437 | |
| D | GLU441 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: |
| Chain | Residue | Details |
| E | ASP84 | |
| F | GLU204 | |
| F | GLU238 | |
| F | HIS241 | |
| G | ASP84 | |
| G | GLU115 | |
| G | HIS118 | |
| G | GLU204 | |
| G | GLU238 | |
| G | HIS241 | |
| H | ASP84 | |
| E | GLU115 | |
| H | GLU115 | |
| H | HIS118 | |
| H | GLU204 | |
| H | GLU238 | |
| H | HIS241 | |
| E | HIS118 | |
| E | GLU204 | |
| E | GLU238 | |
| E | HIS241 | |
| F | ASP84 | |
| F | GLU115 | |
| F | HIS118 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:3R1R |
| Chain | Residue | Details |
| A | LYS9 | |
| C | GLU15 | |
| C | THR55 | |
| C | LYS91 | |
| D | LYS9 | |
| D | GLU15 | |
| D | THR55 | |
| D | LYS91 | |
| A | GLU15 | |
| A | THR55 | |
| A | LYS91 | |
| B | LYS9 | |
| B | GLU15 | |
| B | THR55 | |
| B | LYS91 | |
| C | LYS9 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 28 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:4R1R |
| Chain | Residue | Details |
| A | THR209 | |
| B | ARG262 | |
| B | ARG269 | |
| B | ASN437 | |
| B | GLU441 | |
| B | GLU623 | |
| C | THR209 | |
| C | ASP232 | |
| C | ARG262 | |
| C | ARG269 | |
| C | ASN437 | |
| A | ASP232 | |
| C | GLU441 | |
| C | GLU623 | |
| D | THR209 | |
| D | ASP232 | |
| D | ARG262 | |
| D | ARG269 | |
| D | ASN437 | |
| D | GLU441 | |
| D | GLU623 | |
| A | ARG262 | |
| A | ARG269 | |
| A | ASN437 | |
| A | GLU441 | |
| A | GLU623 | |
| B | THR209 | |
| B | ASP232 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | SITE: Important for hydrogen atom transfer |
| Chain | Residue | Details |
| A | CYS225 | |
| A | CYS462 | |
| B | CYS225 | |
| B | CYS462 | |
| C | CYS225 | |
| C | CYS462 | |
| D | CYS225 | |
| D | CYS462 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | SITE: Important for electron transfer |
| Chain | Residue | Details |
| A | TYR730 | |
| A | TYR731 | |
| B | TYR730 | |
| B | TYR731 | |
| C | TYR730 | |
| C | TYR731 | |
| D | TYR730 | |
| D | TYR731 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | SITE: Interacts with thioredoxin/glutaredoxin |
| Chain | Residue | Details |
| A | CYS754 | |
| A | CYS759 | |
| B | CYS754 | |
| B | CYS759 | |
| C | CYS754 | |
| C | CYS759 | |
| D | CYS754 | |
| D | CYS759 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
| Chain | Residue | Details |
| A | LYS283 | |
| B | LYS283 | |
| C | LYS283 | |
| D | LYS283 |
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 |
