Structure of PDB 8df8 Chain A Binding Site BS03

Receptor Information

>8df8 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

• Ligand ID: PO3
• InChI: InChI=1S/O3P/c1-4(2)3/q-3
• InChIKey: AQSJGOWTSHOLKH-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [O-][P-]([O-])=O
  ACDLabs 10.04: [O-][PH2-]([O-])=O
  OpenEye OEToolkits 1.5.0: [O-][P-](=O)[O-]
• Formula: O3 P
• Name: PHOSPHITE ION
• PDB chain: 8df8 Chain V Residue 101

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): R131 R144
• Binding residue (residue number reindexed from 1): R129 R142
• Annotation score: 1

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