Structure of PDB 8df7 Chain B Binding Site BS01

Receptor Information

>8df7 Chain B (length=850) Species: 2320 (Methanopyrus kandleri)

LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEEL
LELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPAR
YAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRV
DLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDE
IARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDR
LLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQ
DRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRT
LATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAY
RAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASV
EGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEEL
REDGLTDAQIRELKGLKTLESIVGDLEKADELKRKYGSASAVRRLPVEEL
RELGFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYDD
LLELGATPKAAAEIKGPEFKFLLNIEGVGPKLAERILEAVDYDLERLASL
NPEELAEKVEGLGEELAERVVYAARERVESRRKSGRQERSEEEWKEWLER
KVGEGRARRLIEYFGSAGEVGKLVENAEVSKLLEVPGIGDEAVARLVPGY
KTLRDAGLTPAEAERVLKRYGSVSKVQEGATPDELRELGLGDAKIARILG
LRSLVNARLDVDTAYELARRYGSVSAVRAAPVAELRELGLSDRAIARIAG

Ligand information

>8df7 Chain U (length=39)

gcctgcacgaagtaagcatgcttacttcgtgcaggcaca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8df7 Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): V133 K134 P199 R293 P569 K570 S590 L591 K592 G751 K753 T754 S774 S776
• Binding residue (residue number reindexed from 1): V131 K132 P197 R291 P567 K568 S588 L589 K590 G749 K751 T752 S772 S774

Gene Ontology

Molecular Function

• GO:0003677 DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:8df7, PDBe:8df7, PDBj:8df7
• PDBsum: 8df7
• PubMed: 35969036
• UniProt: Q977W1