Structure of PDB 3l4j Chain A Binding Site BS04

Receptor Information

>3l4j Chain A (length=721) Species: 4932 (Saccharomyces cerevisiae)

SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYG
CYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGH
LMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITK
PTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNL
DRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEI
PISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELK
VAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTR
ATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLP
ILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFR
GWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGL
SGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPI
SLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEV
EKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGS
EELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWN
TDLKAFEVGYQEFLQRDAEAR

Ligand information

>3l4j Chain E (length=15)

cgcgaatcgtcatcc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3l4j A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
• Resolution: 2.48 Å
• Binding residue (original residue number in PDB): K477 L479 N480 H533 F642 A647 R650 K651 R781 Y782 I833 G834 G836 W837 S838 K925 K965 P969 N974
• Binding residue (residue number reindexed from 1): K57 L59 N60 H113 F222 A227 R230 K231 R361 Y362 I413 G414 G416 W417 S418 K505 K545 P549 N554

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

External links

• PDB: RCSB:3l4j, PDBe:3l4j, PDBj:3l4j
• PDBsum: 3l4j
• PubMed: 20485342
• UniProt: P06786|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)