Structure of PDB 8df7 Chain A Binding Site BS01

Receptor Information

>8df7 Chain A (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): E41 R108 R109 H281 I285 Y289 S540 A541 S542 R546 R683 R804
• Binding residue (residue number reindexed from 1): E39 R106 R107 H279 I283 Y287 S538 A539 S540 R544 R681 R802

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