Structure of PDB 4j3n Chain B

Receptor sequence

>4j3nB (length=670) Species: 9606 (Homo sapiens)

SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYG
VFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLR
YGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPAKEAKE
YFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRR
LHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKR
NDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQP
IGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRV
EPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPH
PMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYK
EQVLEPMLNPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKL
QTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGML
GAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWK
EAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWK
EDLAAFVEELDKVESQERED

3D structure

• PDB: 4j3n On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs
• Chain: B
• Resolution: 2.3 Å

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 Q778 S818 R820 Y821 I872 G873 G875 W876 T1010 T1012 N1014 S1015	R55 K57 L59 N60 Q68 H116 F177 I182 R185 K186 Q276 S316 R318 Y319 I370 G371 G373 W374 T503 T505 N507 S508
BS02	dna	B	E477 G504 K505 D561 R729 K739 Y773 H775 G776 E870 I872 W947	E29 G56 K57 D113 R227 K237 Y271 H273 G274 E368 I370 W445
BS03	MG	B	D557 D559	D109 D111

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

External links

• PDB: RCSB:4j3n, PDBe:4j3n, PDBj:4j3n
• PDBsum: 4j3n
• PubMed: 24038465
• UniProt: Q02880|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)