5TMC
Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006351 | biological_process | DNA-templated transcription |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| A | 0046983 | molecular_function | protein dimerization activity |
| B | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006351 | biological_process | DNA-templated transcription |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| B | 0046983 | molecular_function | protein dimerization activity |
| C | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| C | 0003677 | molecular_function | DNA binding |
| C | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| C | 0006351 | biological_process | DNA-templated transcription |
| C | 0016740 | molecular_function | transferase activity |
| C | 0016779 | molecular_function | nucleotidyltransferase activity |
| C | 0032549 | molecular_function | ribonucleoside binding |
| C | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| D | 0003677 | molecular_function | DNA binding |
| D | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0006351 | biological_process | DNA-templated transcription |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0016740 | molecular_function | transferase activity |
| D | 0016779 | molecular_function | nucleotidyltransferase activity |
| D | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| E | 0003677 | molecular_function | DNA binding |
| E | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| E | 0006351 | biological_process | DNA-templated transcription |
| E | 0016740 | molecular_function | transferase activity |
| E | 0016779 | molecular_function | nucleotidyltransferase activity |
| E | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| F | 0003677 | molecular_function | DNA binding |
| F | 0003700 | molecular_function | DNA-binding transcription factor activity |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0006352 | biological_process | DNA-templated transcription initiation |
| F | 0006355 | biological_process | regulation of DNA-templated transcription |
| F | 0010468 | biological_process | regulation of gene expression |
| F | 0016987 | molecular_function | sigma factor activity |
| F | 0046872 | molecular_function | metal ion binding |
| F | 2000142 | biological_process | regulation of DNA-templated transcription initiation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue PO4 A 401 |
| Chain | Residue |
| A | THR51 |
| A | LYS83 |
| A | LEU85 |
| A | VAL170 |
| A | ASP202 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 1201 |
| Chain | Residue |
| C | LYS1004 |
| C | PRO793 |
| C | PRO794 |
| C | GLY795 |
| C | GLU796 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue MG D 1601 |
| Chain | Residue |
| C | GLU685 |
| D | G4P1605 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 1602 |
| Chain | Residue |
| D | CYS58 |
| D | CYS60 |
| D | CYS73 |
| D | CYS76 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue ZN D 1603 |
| Chain | Residue |
| D | CYS1112 |
| D | CYS1194 |
| D | GLN1195 |
| D | CYS1201 |
| D | CYS1204 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 1604 |
| Chain | Residue |
| D | ASP739 |
| D | ASP741 |
| D | ASP743 |
| D | HOH1745 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | binding site for residue G4P D 1605 |
| Chain | Residue |
| C | SER878 |
| C | ARG879 |
| D | ASN737 |
| D | ARG783 |
| D | LYS908 |
| D | ARG1029 |
| D | GLU1231 |
| D | GLN1235 |
| D | MG1601 |
| D | MG1606 |
| D | HOH1707 |
| D | HOH1730 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 1606 |
| Chain | Residue |
| D | LYS908 |
| D | G4P1605 |
| D | HOH1707 |
| D | HOH1730 |
Functional Information from PROSITE/UniProt
| site_id | PS00716 |
| Number of Residues | 27 |
| Details | SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL |
| Chain | Residue | Details |
| F | THR382-LEU408 |
| site_id | PS00867 |
| Number of Residues | 8 |
| Details | CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL |
| Chain | Residue | Details |
| F | LEU187-LEU194 |
| site_id | PS01166 |
| Number of Residues | 13 |
| Details | RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV |
| Chain | Residue | Details |
| C | GLY836-VAL848 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 456 |
| Details | Region: {"description":"Alpha N-terminal domain (alpha-NTD)"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 11 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 19 |
| Details | DNA binding: {"description":"H-T-H motif","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 70 |
| Details | Region: {"description":"Sigma-70 factor domain-2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 3 |
| Details | Motif: {"description":"Interaction with polymerase core subunit RpoC"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 35 |
| Details | Region: {"description":"Sigma-70 factor domain-1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 78 |
| Details | Region: {"description":"Sigma-70 factor domain-3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 52 |
| Details | Region: {"description":"Sigma-70 factor domain-4"} |
| Chain | Residue | Details |
