Structure of PDB 5zen Chain A

Receptor sequence

>5zenA (length=708) Species: 9606 (Homo sapiens)

KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKALSFYS
IPEFDEWKKIKYYKGLGTSTAKEAKEYFADMERHRILFRYAGPEDDAAIT
LAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQFLYKHLTYNDFINKELI
LFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEM
SAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPR
YIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAE
GIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKNFKGTIQELGQ
NQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPMLNGTDKTPALI
SDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFD
HMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQARF
ILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEGPDFNYILN
MSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAFVEELDK
VESQERED

3D structure

• PDB: 5zen Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
• Chain: A
• Resolution: 2.75 Å

Enzymatic activity

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	E477 G504 K505 D561 R729 K739 Y773 H775 G776 N786 I872 R945 W947	E26 G53 K54 D110 R259 K269 Y303 H305 G306 N316 I402 R475 W477
BS02	dna	A	L507 N508 N520 H564 I674 R677 K678 I872 G873 T874 G875 W876 A877 T1010 T1012 N1014 S1015	L56 N57 N69 H113 I208 R211 K212 I402 G403 T404 G405 W406 A407 T540 T542 N544 S545
BS03	MN	A	D557 D559	D106 D108

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