Structure of PDB 5zad Chain B

Receptor sequence

>5zadB (length=729) Species: 9606 (Homo sapiens) [Search protein sequence]

KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKASKNKQ
ELSFYSIPEFDEWKKHIWKIKYYKGLGTSTAKEAKEYFADMERHRILFRY
AGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQFLYGTAT
KHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKR
EVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQF
GTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEW
YIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLP
NYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVL
EPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFK
LQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGM
LGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAW
KEAQEKAAEEDEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLK
RKSPSDLWKEDLAAFVEELDKVESQERED

3D structure

PDB

5zad Increasing the distance between two monomers of topoisomerase II beta under the action of antitumor agent 4 beta-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin.

Chain

Resolution

2.54 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)	Binding affinity
BS01	dna	B	E477 G504 K505 D561 R729 K739 Y773 H775 G776 T783 N786 I872 W947	E26 G53 K54 D110 R273 K283 Y317 H319 G320 T327 N330 I416 W491
BS02	dna	B	D479 R503 K505 L507 N508 N520 H564 F669 I674 R677 K678 Q778 I872 G873 T874 G875 W876 A877 K879 T1010 T1012 N1014 S1015	D28 R52 K54 L56 N57 N69 H113 F213 I218 R221 K222 Q322 I416 G417 T418 G419 W420 A421 K423 T554 T556 N558 S559

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:5zad, PDBe:5zad, PDBj:5zad
PDBsum	5zad
PubMed	30297860
UniProt	Q02880\|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)

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