3HND
Crystal structure of human ribonucleotide reductase 1 bound to the effector TTP and substrate GDP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000731 | biological_process | DNA synthesis involved in DNA repair |
| 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 | 0005635 | cellular_component | nuclear envelope |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005829 | cellular_component | cytosol |
| A | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| A | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
| A | 0006264 | biological_process | mitochondrial DNA replication |
| A | 0006281 | biological_process | DNA repair |
| A | 0008584 | biological_process | male gonad development |
| A | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| A | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| A | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| A | 0010212 | biological_process | response to ionizing radiation |
| A | 0010971 | biological_process | positive regulation of G2/M transition of mitotic cell cycle |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0017076 | molecular_function | purine nucleotide binding |
| A | 0021846 | biological_process | cell proliferation in forebrain |
| A | 0034451 | cellular_component | centriolar satellite |
| A | 0036064 | cellular_component | ciliary basal body |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042995 | cellular_component | cell projection |
| A | 0043025 | cellular_component | neuronal cell body |
| A | 0051290 | biological_process | protein heterotetramerization |
| A | 0060041 | biological_process | retina development in camera-type eye |
| A | 0061731 | molecular_function | ribonucleoside-diphosphate reductase activity |
| A | 0070318 | biological_process | positive regulation of G0 to G1 transition |
| A | 0097718 | molecular_function | disordered domain specific binding |
| A | 1900087 | biological_process | positive regulation of G1/S transition of mitotic cell cycle |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000731 | biological_process | DNA synthesis involved in DNA repair |
| 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 | 0005635 | cellular_component | nuclear envelope |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005829 | cellular_component | cytosol |
| B | 0005971 | cellular_component | ribonucleoside-diphosphate reductase complex |
| B | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
| B | 0006264 | biological_process | mitochondrial DNA replication |
| B | 0006281 | biological_process | DNA repair |
| B | 0008584 | biological_process | male gonad development |
| B | 0009185 | biological_process | ribonucleoside diphosphate metabolic process |
| B | 0009263 | biological_process | deoxyribonucleotide biosynthetic process |
| B | 0009265 | biological_process | 2'-deoxyribonucleotide biosynthetic process |
| B | 0010212 | biological_process | response to ionizing radiation |
| B | 0010971 | biological_process | positive regulation of G2/M transition of mitotic cell cycle |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0017076 | molecular_function | purine nucleotide binding |
| B | 0021846 | biological_process | cell proliferation in forebrain |
| B | 0034451 | cellular_component | centriolar satellite |
| B | 0036064 | cellular_component | ciliary basal body |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042995 | cellular_component | cell projection |
| B | 0043025 | cellular_component | neuronal cell body |
| B | 0051290 | biological_process | protein heterotetramerization |
| B | 0060041 | biological_process | retina development in camera-type eye |
| B | 0061731 | molecular_function | ribonucleoside-diphosphate reductase activity |
| B | 0070318 | biological_process | positive regulation of G0 to G1 transition |
| B | 0097718 | molecular_function | disordered domain specific binding |
| B | 1900087 | biological_process | positive regulation of G1/S transition of mitotic cell cycle |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG A 801 |
| Chain | Residue |
| A | TTP802 |
| site_id | AC2 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TTP A 802 |
| Chain | Residue |
| A | GLY264 |
| A | SER269 |
| A | ASN270 |
| A | MG801 |
| A | HOH910 |
| B | LYS243 |
| B | TYR285 |
| B | VAL286 |
| B | ASP287 |
| B | GLN288 |
| A | ASP226 |
| B | GLY289 |
| A | SER227 |
| A | ILE228 |
| A | GLU229 |
| A | ILE255 |
| A | ARG256 |
| A | ILE262 |
| A | ALA263 |
| site_id | AC3 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE GDP A 803 |
| Chain | Residue |
| A | SER202 |
| A | SER217 |
| A | CYS218 |
| A | ALA245 |
| A | GLY246 |
| A | GLY247 |
| A | GLY295 |
| A | ASN427 |
| A | LEU428 |
| A | CYS429 |
| A | GLU431 |
| A | PRO603 |
| A | THR604 |
| A | ALA605 |
| A | SER606 |
| A | THR607 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 805 |
| Chain | Residue |
| A | ILE136 |
| A | TYR137 |
| A | ASP138 |
| B | LYS382 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 806 |
| Chain | Residue |
| A | ASN614 |
| A | GLU615 |
| A | THR621 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 807 |
| Chain | Residue |
| A | SER687 |
| A | GLN688 |
| A | LYS689 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MG B 801 |
| Chain | Residue |
| B | TTP802 |
| site_id | AC8 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE TTP B 802 |
| Chain | Residue |
| A | LYS243 |
| A | TYR285 |
| A | VAL286 |
| A | ASP287 |
| A | GLN288 |
| A | GLY289 |
| B | ASP226 |
| B | SER227 |
| B | ILE228 |
| B | ILE255 |
| B | ARG256 |
| B | ILE262 |
| B | ALA263 |
| B | GLY264 |
| B | SER269 |
| B | ASN270 |
| B | MG801 |
| site_id | AC9 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE GDP B 803 |
| Chain | Residue |
| B | ALA201 |
| B | SER202 |
| B | SER217 |
| B | CYS218 |
| B | ALA245 |
| B | GLY246 |
| B | GLY247 |
| B | ARG293 |
| B | ASN427 |
| B | LEU428 |
| B | CYS429 |
| B | GLU431 |
| B | PRO603 |
| B | THR604 |
| B | ALA605 |
| B | SER606 |
| B | THR607 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 B 804 |
| Chain | Residue |
| B | SER687 |
| B | GLN688 |
| B | LYS689 |
Functional Information from PROSITE/UniProt
| site_id | PS00089 |
| Number of Residues | 23 |
| Details | RIBORED_LARGE Ribonucleotide reductase large subunit signature. WkvLkekiakyGIRNsllIApmP |
| Chain | Residue | Details |
| A | TRP581-PRO603 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250 |
| Chain | Residue | Details |
| A | ASN427 | |
| A | GLU431 | |
| B | ASN427 | |
| B | GLU431 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: Cysteine radical intermediate => ECO:0000250 |
| Chain | Residue | Details |
| A | CYS429 | |
| B | CYS429 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0007744|PDB:3HNE |
| Chain | Residue | Details |
| A | LYS5 | |
| B | GLU11 | |
| B | THR53 | |
| B | ASP57 | |
| B | ASP226 | |
| B | LYS243 | |
| B | ARG256 | |
| B | ALA263 | |
| A | GLU11 | |
| A | THR53 | |
| A | ASP57 | |
| A | ASP226 | |
| A | LYS243 | |
| A | ARG256 | |
| A | ALA263 | |
| B | LYS5 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0007744|PDB:3HND |
| Chain | Residue | Details |
| A | SER202 | |
| B | THR604 | |
| A | SER217 | |
| A | ASN427 | |
| A | GLU431 | |
| A | THR604 | |
| B | SER202 | |
| B | SER217 | |
| B | ASN427 | |
| B | GLU431 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | SITE: Important for hydrogen atom transfer => ECO:0000250 |
| Chain | Residue | Details |
| A | CYS218 | |
| A | CYS444 | |
| B | CYS218 | |
| B | CYS444 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | SITE: Important for electron transfer => ECO:0000250 |
| Chain | Residue | Details |
| A | TYR737 | |
| A | TYR738 | |
| B | TYR737 | |
| B | TYR738 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | SITE: Interacts with thioredoxin/glutaredoxin => ECO:0000250 |
| Chain | Residue | Details |
| A | CYS787 | |
| A | CYS790 | |
| B | CYS787 | |
| B | CYS790 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS17 | |
| A | LYS376 | |
| B | LYS17 | |
| B | LYS376 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR751 | |
| B | THR751 |
