Structure of PDB 5gwk Chain B

Receptor sequence

>5gwkB (length=724) Species: 9606 (Homo sapiens) [Search protein sequence]

KGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQ
EMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHR
IQFKYSGPEDDAAISLAFSKKQIDDRKEWLTNFMEDRRQRKLLGLPEDYL
YGQTTTYLTYNDFINKELILFSNSDNERSIPSMVDGLKPGQRKVLFTCFK
RNDKREVKVAQLAGSVAEMSSYHHGEMSLMMTIINLAQNFVGSNNLNLLQ
PIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDDHTLKFLYDDNQR
VEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEEP
LPMLPSYKNFKGTIEELAPNQYVISGEVAILNSTTIEISELPVRTWTQTY
KEQVLEPMLNGTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVGLHKV
FKLQTSLTCNSMVLFDHVGCLKKYDTVLDILRDFFELRLKYYGLRKEWLL
GMLGAESAKLNNQARFILEKIDGKIIIENKPKKELIKVLIQRGYDSDPVK
AWKEAQQSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELDTLKRKSP
SDLWKEDLATFIEELEAVEAKEKQ

3D structure

PDB

5gwk Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry

Chain

Resolution

3.152 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	K489 L491 N492 Q500 H548 F653 I658 R661 Y805 I856 G857 T858 G859 W860 S861 S994 T996 S999	K54 L56 N57 Q65 H113 F218 I223 R226 Y370 I421 G422 T423 G424 W425 S426 S556 T558 S561
BS02	dna	B	E461 G488 D545 R713 Y757 H759 G760 T767 N770 E854 I856 W931	E26 G53 D110 R278 Y322 H324 G325 T332 N335 E419 I421 W496
BS03	dna	B	K440 M762	K5 M327
BS04	MG	B	D541 D543	D106 D108
BS05	EVP	B	G462 D463 R487 M766	G27 D28 R52 M331	BindingDB: EC50=810nM,IC50=56000nM

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:5gwk, PDBe:5gwk, PDBj:5gwk
PDBsum	5gwk
PubMed	28977631
UniProt	P11388\|TOP2A_HUMAN DNA topoisomerase 2-alpha (Gene Name=TOP2A)

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