Structure of PDB 5zqf Chain A

Receptor sequence

>5zqfA (length=708) Species: 9606 (Homo sapiens) [Search protein sequence]

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

3D structure

PDB

5zqf Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Chain

Resolution

3.873 Å

3D
structure

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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)
BS01	dna	A	E477 G504 K505 S513 D561 R729 K739 Y773 H775 G776 T783 N786 K814 I872 R945 W947	E26 G53 K54 S62 D110 R259 K269 Y303 H305 G306 T313 N316 K344 I402 R475 W477
BS02	dna	A	R503 K505 L507 N508 H564 R677 K678 I872 G873 T874 G875 W876 A877 T1010 L1011 T1012 N1014 S1015	R52 K54 L56 N57 H113 R211 K212 I402 G403 T404 G405 W406 A407 T540 L541 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

View graph for
Molecular Function

View graph for
Biological Process

External links

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

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