5D4E
Crystal structure of Thermus thermophilus product complex for transcription initiation with 3'-dephosphate-CoA and CTP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| 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 | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| A | 0046983 | molecular_function | protein dimerization activity |
| 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 | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| B | 0046983 | molecular_function | protein dimerization activity |
| C | 0003677 | molecular_function | DNA binding |
| C | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| C | 0006351 | biological_process | DNA-templated transcription |
| C | 0032549 | molecular_function | ribonucleoside binding |
| C | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| D | 0000287 | molecular_function | magnesium ion binding |
| 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 | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| E | 0003677 | molecular_function | DNA binding |
| E | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| E | 0006351 | biological_process | DNA-templated transcription |
| 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 | 2000142 | biological_process | regulation of DNA-templated transcription initiation |
| K | 0003677 | molecular_function | DNA binding |
| K | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| K | 0005515 | molecular_function | protein binding |
| K | 0005737 | cellular_component | cytoplasm |
| K | 0006351 | biological_process | DNA-templated transcription |
| K | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| K | 0046983 | molecular_function | protein dimerization activity |
| L | 0003677 | molecular_function | DNA binding |
| L | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| L | 0005515 | molecular_function | protein binding |
| L | 0005737 | cellular_component | cytoplasm |
| L | 0006351 | biological_process | DNA-templated transcription |
| L | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| L | 0046983 | molecular_function | protein dimerization activity |
| M | 0003677 | molecular_function | DNA binding |
| M | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| M | 0006351 | biological_process | DNA-templated transcription |
| M | 0032549 | molecular_function | ribonucleoside binding |
| M | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| N | 0000287 | molecular_function | magnesium ion binding |
| N | 0003677 | molecular_function | DNA binding |
| N | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| N | 0005515 | molecular_function | protein binding |
| N | 0006351 | biological_process | DNA-templated transcription |
| N | 0008270 | molecular_function | zinc ion binding |
| N | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| O | 0003677 | molecular_function | DNA binding |
| O | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| O | 0006351 | biological_process | DNA-templated transcription |
| O | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| P | 0003677 | molecular_function | DNA binding |
| P | 0003700 | molecular_function | DNA-binding transcription factor activity |
| P | 0005737 | cellular_component | cytoplasm |
| P | 0006352 | biological_process | DNA-templated transcription initiation |
| P | 0006355 | biological_process | regulation of DNA-templated transcription |
| P | 0010468 | biological_process | regulation of gene expression |
| P | 0016987 | molecular_function | sigma factor activity |
| P | 2000142 | biological_process | regulation of DNA-templated transcription initiation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue MG B 2001 |
| Chain | Residue |
| B | ARG30 |
| B | ASP183 |
| B | ASP191 |
| B | ASP193 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 2001 |
| Chain | Residue |
| D | CYS1112 |
| D | CYS1194 |
| D | CYS1201 |
| D | CYS1204 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue ZN D 2002 |
| Chain | Residue |
| D | CYS60 |
| D | LYS62 |
| D | CYS73 |
| D | CYS76 |
| D | CYS58 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue MG D 2003 |
| Chain | Residue |
| D | ASP739 |
| D | ASP741 |
| D | ASP743 |
| D | C5P2005 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue MG D 2004 |
| Chain | Residue |
| B | ASP168 |
| D | LYS840 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue DPO D 2006 |
| Chain | Residue |
| C | ARG879 |
| D | ASP739 |
| D | ARG1029 |
| D | MG2007 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue MG D 2007 |
| Chain | Residue |
| C | ARG879 |
| D | ASP739 |
| D | DPO2006 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue MG F 2001 |
| Chain | Residue |
| F | ALA292 |
| F | GLY296 |
| F | TRP299 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue MG L 1601 |
| Chain | Residue |
| L | ASP168 |
| N | LYS840 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN N 1601 |
| Chain | Residue |
| N | CYS1112 |
| N | CYS1194 |
| N | CYS1201 |
| N | CYS1204 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN N 1602 |
| Chain | Residue |
| N | CYS58 |
| N | CYS60 |
| N | CYS73 |
| N | CYS76 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue MG N 1603 |
| Chain | Residue |
| N | ASP739 |
| N | ASP741 |
| N | ASP743 |
| N | C5P1604 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue DPO N 1605 |
| Chain | Residue |
| M | ARG879 |
| N | ASP739 |
| N | ARG1029 |
| N | MG1606 |
| N | HOH2140 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue MG N 1606 |
| Chain | Residue |
| M | GLU685 |
| M | HOH1216 |
| N | ASP739 |
| N | DPO1605 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue MG P 2001 |
| Chain | Residue |
| P | ALA292 |
| P | GLY296 |
| P | TRP299 |
| site_id | AD7 |
| Number of Residues | 12 |
| Details | binding site for Di-nucleotide C D 2005 and COD D 2008 |
| Chain | Residue |
| C | GLN567 |
| C | LYS838 |
| C | LYS846 |
| C | HIS999 |
| D | ARG704 |
| D | ASP741 |
| D | ASP743 |
| D | MG2003 |
| D | HOH2136 |
| G | DG15 |
| G | DT16 |
| G | DA17 |
| site_id | AD8 |
| Number of Residues | 12 |
| Details | binding site for Di-nucleotide C N 1605 and COD N 1608 |
| Chain | Residue |
| M | GLN567 |
| M | LYS838 |
| M | LYS846 |
| M | TYR998 |
| M | HIS999 |
| N | ARG704 |
| N | ASP741 |
| N | ASP743 |
| N | MG1603 |
| R | DG15 |
| R | DT16 |
| R | DA17 |
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 | 22 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 38 |
| 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_FI4 |
| Number of Residues | 140 |
| Details | Region: {"description":"Sigma-70 factor domain-2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | Motif: {"description":"Interaction with polymerase core subunit RpoC"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 70 |
| Details | Region: {"description":"Sigma-70 factor domain-1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 156 |
| Details | Region: {"description":"Sigma-70 factor domain-3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 104 |
| Details | Region: {"description":"Sigma-70 factor domain-4"} |
| Chain | Residue | Details |
