Structure of PDB 5zrf Chain B Binding Site BS01

Receptor Information

>5zrf Chain B (length=671) Species: 9606 (Homo sapiens)

SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYG
VFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLR
YGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPAKEAKE
YFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRR
LHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKR
NDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQP
IGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRV
EPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPH
PMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYK
EQVLEPMLNGPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFK
LQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGM
LGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAW
KEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLW
KEDLAAFVEELDKVESQERED

Ligand information

>5zrf Chain D (length=12)

ugcagcucggcu

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zrf Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): R503 K505 L507 N508 Q516 H564 F669 I674 R677 K678 R820 Y821 I872 G873 G875 W876 T1010 L1011 T1012 N1014 S1015
• Binding residue (residue number reindexed from 1): R55 K57 L59 N60 Q68 H116 F177 I182 R185 K186 R318 Y319 I370 G371 G373 W374 T504 L505 T506 N508 S509

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006265 DNA topological change

External links

• PDB: RCSB:5zrf, PDBe:5zrf, PDBj:5zrf
• PDBsum: 5zrf
• PubMed: 30082834
• UniProt: Q02880|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)