5ZRF
Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0006259 | biological_process | DNA metabolic process |
| A | 0006265 | biological_process | DNA topological change |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0006259 | biological_process | DNA metabolic process |
| B | 0006265 | biological_process | DNA topological change |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 1301 |
| Chain | Residue |
| A | ASP557 |
| A | ASP559 |
| A | HOH1462 |
| A | HOH1496 |
| A | HOH1577 |
| C | HOH102 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | binding site for residue MG A 1302 |
| Chain | Residue |
| A | ASN867 |
| A | GLY868 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue MG B 1301 |
| Chain | Residue |
| B | GLY868 |
| B | HOH1557 |
| E | HOH101 |
| B | ASN867 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 1302 |
| Chain | Residue |
| B | ASP557 |
| B | ASP559 |
| B | HOH1424 |
| B | HOH1531 |
| E | HOH104 |
| E | HOH114 |
| site_id | AC5 |
| Number of Residues | 12 |
| Details | binding site for residue EVP D 101 |
| Chain | Residue |
| B | GLY478 |
| B | ASP479 |
| B | ARG503 |
| B | GLN778 |
| B | MET782 |
| D | DA12 |
| D | DG13 |
| D | HOH505 |
| D | HOH510 |
| E | DC8 |
| F | IU9 |
| F | DG10 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue MG D 102 |
| Chain | Residue |
| D | HOH507 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | binding site for residue EVP F 1301 |
| Chain | Residue |
| A | GLY478 |
| A | ASP479 |
| A | ARG503 |
| A | MET782 |
| C | DC8 |
| C | HOH107 |
| D | IU9 |
| D | DG10 |
| F | DA12 |
| F | DG13 |
| F | HOH1404 |
| F | HOH1417 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue MG F 1302 |
| Chain | Residue |
| A | HOH1604 |
| F | HOH1402 |
| F | HOH1409 |
| F | HOH1415 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for Di-nucleotide IU D 9 and DG D 10 |
| Chain | Residue |
| A | ASP479 |
| B | ARG820 |
| B | TYR821 |
| D | DC11 |
| F | DG10 |
| F | DC11 |
| F | DA12 |
| F | EVP1301 |
| site_id | AD1 |
| Number of Residues | 14 |
| Details | binding site for Di-nucleotide DC D 14 and IU D 15 |
| Chain | Residue |
| B | LYS505 |
| B | ILE506 |
| B | LEU507 |
| B | ASN508 |
| B | GLN516 |
| B | HIS564 |
| D | DG13 |
| D | DC16 |
| D | HOH503 |
| D | HOH506 |
| D | HOH513 |
| E | DG5 |
| E | DA6 |
| E | DG7 |
| site_id | AD2 |
| Number of Residues | 20 |
| Details | binding site for Di-nucleotide IU D 15 and DC D 16 |
| Chain | Residue |
| B | ILE506 |
| B | LEU507 |
| B | ASN508 |
| B | HIS564 |
| B | PHE669 |
| B | ILE872 |
| B | GLY873 |
| B | THR874 |
| B | HOH1406 |
| D | DC14 |
| D | DG17 |
| D | HOH503 |
| D | HOH504 |
| D | HOH506 |
| D | HOH508 |
| D | HOH513 |
| E | DC4 |
| E | DG5 |
| E | DA6 |
| E | DG7 |
| site_id | AD3 |
| Number of Residues | 12 |
| Details | binding site for Di-nucleotide DC D 19 and IU D 20 |
| Chain | Residue |
| E | DA1 |
| E | DG2 |
| A | ASP897 |
| A | LEU899 |
| B | LYS879 |
| B | THR1010 |
| B | LEU1011 |
| B | THR1012 |
| B | ASN1014 |
| D | DG18 |
| D | HOH501 |
| D | HOH502 |
| site_id | AD4 |
| Number of Residues | 8 |
| Details | binding site for Di-nucleotide IU F 9 and DG F 10 |
| Chain | Residue |
| A | TYR821 |
| B | ASP479 |
| D | DG10 |
| D | DC11 |
| D | DA12 |
| D | EVP101 |
| F | DC11 |
| F | HOH1401 |
| site_id | AD5 |
| Number of Residues | 15 |
| Details | binding site for Di-nucleotide DC F 14 and IU F 15 |
| Chain | Residue |
| A | LYS505 |
| A | ILE506 |
| A | LEU507 |
| A | ASN508 |
| A | GLN516 |
| A | HIS564 |
| C | DG5 |
| C | DA6 |
| C | DG7 |
| F | DG13 |
| F | DC16 |
| F | HOH1405 |
| F | HOH1406 |
| F | HOH1418 |
| F | HOH1419 |
| site_id | AD6 |
| Number of Residues | 20 |
| Details | binding site for Di-nucleotide IU F 15 and DC F 16 |
| Chain | Residue |
| A | ILE506 |
| A | LEU507 |
| A | ASN508 |
| A | HIS564 |
| A | PHE669 |
| A | ILE872 |
| A | GLY873 |
| A | THR874 |
| A | HOH1407 |
| C | DG5 |
| C | DA6 |
| C | DG7 |
| F | DC14 |
| F | DG17 |
| F | HOH1403 |
| F | HOH1405 |
| F | HOH1406 |
| F | HOH1412 |
| F | HOH1418 |
| F | HOH1419 |
| site_id | AD7 |
| Number of Residues | 9 |
| Details | binding site for Di-nucleotide DC F 19 and IU F 20 |
| Chain | Residue |
| A | LYS879 |
| A | THR1010 |
| A | LEU1011 |
| A | THR1012 |
| A | ASN1014 |
| A | SER1015 |
| C | DA1 |
| C | DG2 |
| F | DG18 |
Functional Information from PROSITE/UniProt
| site_id | PS00177 |
| Number of Residues | 9 |
| Details | TOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKS |
| Chain | Residue | Details |
| A | LEU475-SER483 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 234 |
| Details | Domain: {"description":"Toprim","evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | Region: {"description":"Interaction with DNA"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 20 |
| Details | Motif: {"description":"Nuclear export signal"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Active site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU01384","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21778401","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21778401","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | Site: {"description":"Interaction with DNA"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Site: {"description":"Interaction with DNA","evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Site: {"description":"Transition state stabilizer"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Site: {"description":"Important for DNA bending; intercalates between base pairs of target DNA"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"25772364","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 10 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
