Brand  (β version)

PDB ID: 5ZRF

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Ligands
Code Name Style Show Link
EVP (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-D][1,3]dioxol -5-yl 4,6-O-[(1r)-ethylidene]-beta-D-glucopyranoside PoSSuM
MG Magnesium ion PoSSuM
Non-standard Residues
Code Name Show
IU 5-iodouridine-5'-monophosphate
Glycosylation
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Modification
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Structure summary

Code : 5ZRF   PDBj   RCSB PDB   PDBe
Header : ISOMERASE/DNA
Title : Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21
Release Data : 2018-08-08
Compound :
mol_id molecule chains synonym
1 DNA topoisomerase 2-beta A,B DNA topoisomerase II,beta isozyme
ec: 5.99.1.3
mol_id molecule chains
2 DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') C,E
mol_id molecule chains
3 DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3') D,F
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: TOP2B
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET51b
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Chen, S.F., Wang, Y.R., Wu, C.C., Chan, N.L.
Keywords : Type II topoisomerase, Anti-cancer drug, TopoII cleavage complex, Isomerase-DNA complex, ISOMERASE-DNA-ISOMERASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 2.30 Å )
Citation :

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Chen, S.F.,Huang, N.L.,Lin, J.H.  et al.
(2018)  Nat Commun  9 : 3085 - 3085

PubMed: 30082834
DOI: 10.1038/s41467-018-05406-y

Reaction

Chain : A, B
UniProt : Q02880 (TOP2B_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 PROSITE- ProRule:PRU00995, PubMed:10684600
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