Structure of PDB 5zrf Chain A

Receptor sequence

>5zrfA (length=669) Species: 9606 (Homo sapiens) [Search protein sequence]

KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITKEAKEYFADM
ERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHKHL
TYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVK
VAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTR
LHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRVEPEWYIP
IIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYK
NFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYKEQVLEPM
LNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQT
TLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGA
ESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEA
QEGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKE
DLAAFVEELDKVESQERED

3D structure

PDB

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

Chain

Resolution

2.3 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	A	E477 G504 K505 D561 R729 K739 Y773 H775 G776 T783 N786 I872 W947	E26 G53 K54 D110 R220 K230 Y264 H266 G267 T274 N277 I363 W438
BS02	dna	A	R503 K505 L507 N508 Q516 H564 F669 R677 K678 Y821 I872 G873 T874 G875 W876 A877 K879 T1010 L1011 T1012 N1014 S1015	R52 K54 L56 N57 Q65 H113 F172 R180 K181 Y312 I363 G364 T365 G366 W367 A368 K370 T501 L502 T503 N505 S506
BS03	MG	A	D557 D559	D106 D108
BS04	EVP	A	G478 D479 R503 M782	G27 D28 R52 M273	BindingDB: IC50=70nM,EC50=>70000nM

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

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