9GDB
RNAP-TopoI complex on bubble scaffold - consensus reconstruction
This is a non-PDB format compatible entry.
Functional Information from PROSITE/UniProt
| site_id | PS00396 |
| Number of Residues | 15 |
| Details | TOPO_IA_1 Topoisomerase (Topo) IA-type active site signature. QrLYEagy.........ITYmRTD |
| Chain | Residue | Details |
| F | GLN309-ASP323 |
| site_id | PS01166 |
| Number of Residues | 13 |
| Details | RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV |
| Chain | Residue | Details |
| C | GLY1063-VAL1075 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | Region: {"description":"Required for interaction with Crp at class II promoters"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 11 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"32871103","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4MEX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4MEY","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 417 |
| Details | Domain: {"description":"Topo IA-type catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 31 |
| Details | Zinc finger: {"description":"C4-type 1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 27 |
| Details | Zinc finger: {"description":"C4-type 2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 25 |
| Details | Zinc finger: {"description":"C4-type 3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 5 |
| Details | Region: {"description":"Interaction with DNA"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | Active site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21482796","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8114910","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9497321","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00952","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 8 |
| Details | Site: {"description":"Interaction with DNA"} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 7 |
| Details | M-CSA 366 |
| Chain | Residue | Details |
| F | GLU9 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay |
| F | ASP111 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay |
| F | ASP113 | metal ligand |
| F | GLU115 | metal ligand |
| F | TYR319 | activator, covalently attached, hydrogen bond acceptor, nucleofuge, nucleophile, proton acceptor, proton donor |
| F | ARG321 | electrostatic stabiliser |
| F | HIS365 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, proton acceptor, proton donor |
