Structure of PDB 8dfb Chain B Binding Site BS01

Receptor Information
>8dfb Chain B (length=850) Species: 2320 (Methanopyrus kandleri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEEL
LELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPAR
YAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGRV
DLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHDE
IARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRDR
LLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKLQ
DRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNRT
LATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEAY
RAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLASV
EGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEEL
REDGLTDAQIRELKGLKTLESIVGDLEKADELKRKYGSASAVRRLPVEEL
RELGFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYDD
LLELGATPKAAAEIKGPEFKFLLNIEGVGPKLAERILEAVDYDLERLASL
NPEELAEKVEGLGEELAERVVYAARERVESRRKSGRQERSEEEWKEWLER
KVGEGRARRLIEYFGSAGEVGKLVENAEVSKLLEVPGIGDEAVARLVPGY
KTLRDAGLTPAEAERVLKRYGSVSKVQEGATPDELRELGLGDAKIARILG
LRSLVNARLDVDTAYELARRYGSVSAVRAAPVAELRELGLSDRAIARIAG
Ligand information
>8dfb Chain U (length=40) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gcctgcacgaagtaagcattgcttacttcgtgcaggcaca
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8dfb Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
Resolution3.17 Å
Binding residue
(original residue number in PDB)		E41 K47 R83 R108 V133 K134 D201 V211 R287 R288 R293 P569 L591 K592 G751 K753 T754 S774 S776
Binding residue
(residue number reindexed from 1)		E39 K45 R81 R106 V131 K132 D199 V209 R285 R286 R291 P567 L589 K590 G749 K751 T752 S772 S774
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0006281 DNA repair

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Molecular Function
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Biological Process
External links
PDB RCSB:8dfb, PDBe:8dfb, PDBj:8dfb
PDBsum8dfb
PubMed35969036
UniProtQ977W1

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