Structure of PDB 5zrf Chain B

Receptor sequence

>5zrfB (length=671) Species: 9606 (Homo sapiens) [Search protein sequence]

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

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	B	R503 K505 L507 N508 Q516 H564 F669 I674 R677 K678 R820 Y821 I872 G873 G875 W876 T1010 L1011 T1012 N1014 S1015	R55 K57 L59 N60 Q68 H116 F177 I182 R185 K186 R318 Y319 I370 G371 G373 W374 T504 L505 T506 N508 S509
BS02	dna	B	E477 G504 K505 D561 R729 K739 Y773 H775 G776 T783 N786 E870 I872 W947	E29 G56 K57 D113 R227 K237 Y271 H273 G274 T281 N284 E368 I370 W445
BS03	MG	B	D557 D559	D109 D111
BS04	EVP	B	G478 D479 R503 M782	G30 D31 R55 M280	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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