Structure of PDB 5gwk Chain B Binding Site BS04

Receptor Information
>5gwk Chain B (length=724) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQ
EMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHR
IQFKYSGPEDDAAISLAFSKKQIDDRKEWLTNFMEDRRQRKLLGLPEDYL
YGQTTTYLTYNDFINKELILFSNSDNERSIPSMVDGLKPGQRKVLFTCFK
RNDKREVKVAQLAGSVAEMSSYHHGEMSLMMTIINLAQNFVGSNNLNLLQ
PIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDDHTLKFLYDDNQR
VEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEEP
LPMLPSYKNFKGTIEELAPNQYVISGEVAILNSTTIEISELPVRTWTQTY
KEQVLEPMLNGTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVGLHKV
FKLQTSLTCNSMVLFDHVGCLKKYDTVLDILRDFFELRLKYYGLRKEWLL
GMLGAESAKLNNQARFILEKIDGKIIIENKPKKELIKVLIQRGYDSDPVK
AWKEAQQSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELDTLKRKSP
SDLWKEDLATFIEELEAVEAKEKQ
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5gwk Chain B Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5gwk Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Resolution3.152 Å
Binding residue
(original residue number in PDB)		D541 D543
Binding residue
(residue number reindexed from 1)		D106 D108
Annotation score4
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5gwk, PDBe:5gwk, PDBj:5gwk
PDBsum5gwk
PubMed28977631
UniProtP11388|TOP2A_HUMAN DNA topoisomerase 2-alpha (Gene Name=TOP2A)

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