Structure of PDB 8df8 Chain B Binding Site BS01

Receptor Information

>8df8 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

>8df8 Chain U (length=39)

cctgcacgaagtaagcatatgcttacttcgtgcaggcac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8df8 Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
• Resolution: 2.92 Å
• Binding residue (original residue number in PDB): R37 R108 R131 V133 K134 R144 D201 R293 P569 K570 G751 K753 T754 V775 S776
• Binding residue (residue number reindexed from 1): R35 R106 R129 V131 K132 R142 D199 R291 P567 K568 G749 K751 T752 V773 S774

Gene Ontology

Molecular Function

• GO:0003677 DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:8df8, PDBe:8df8, PDBj:8df8
• PDBsum: 8df8
• PubMed: 35969036
• UniProt: Q977W1