Structure of PDB 9ezy Chain B

Receptor sequence

>9ezyB (length=657) Species: 666 (Vibrio cholerae)

QGPLSTLIEQISIDTDWVDRSFAIYCVSYKGIDFSERPKRLVTLASETYK
SGSVYCLVKGANKEACYWVLLPKDSKLDLKDTSLAIKPSSAAELPTWQLA
RLLIKAIPKVLEGLYYLVKSKKLPKDHSGYELTTVEIDLAPCAALGFKQT
LSMGTKTFSPLSWQKKARFATRYQLDDVGKLVSKSIKGDYIKKPLYSNAK
NRIQAIDITKESYSGFQLSKVGILEQFMQDLKQAYGDSVSVKLQRIPGEK
HRFVSDTIVKNHYVGLFDALKEHRLVICDLTENQDTDAALTLLHGIEHLD
INAEIAEVPIRGALNILIVGNKDTYKSDEEDPYQVYRKKYQDTVFQSCYP
ERLWNRQGQPNRHVVEVLLKELLIKLEVHTRKHLIEYPSGPERCVYYMPQ
RPKDESSEVRDEPWPVYASKLVGDEWQYTQATQEELEDIELDLGNDKRHV
FHGFERSPVIYWPETGDYAIFIDTGIQMLPEFEAVAERLRELKEGRSQDV
PIALLAQFIEENPESKVINKLRAILSEWDDVAPLPFDEFSTIAYKSSDEK
QFYDWLREQGFFLKTSIRGQSEGFFNASLGFFYNREQGMYFAGGKGSPQS
KIETFSHLYLIKHSFDALPEEVENLFDVYHLRHRLPTVTPYPFKHLREYV
EMQRFRS

3D structure

• PDB: 9ezy Molecular mechanism of plasmid elimination by the DdmDE defense system.
• Chain: B
• Resolution: 2.56 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	B	K69 N72 T177 T179 K230 N231 R232 K250 K352 D361 Y363 Q376 S377 C378 Y379 R382 V394 V397 E401 Q507 T634 F635 H637 Y639 L661 R662 V668 T669 K674	K59 N62 T155 T157 K200 N201 R202 K220 K322 D331 Y333 Q346 S347 C348 Y349 R352 V364 V367 E371 Q477 T604 F605 H607 Y609 L631 R632 V638 T639 K644
BS02	dna	B	A55 S56 L67 K69 R111 E134 K214 N228 A229 K230 R232 R392 H393 R431 F484 K575 S576 S577 K625 Q629 E633 H663 R664	A45 S46 L57 K59 R101 E112 K184 N198 A199 K200 R202 R362 H363 R401 F454 K545 S546 S547 K595 Q599 E603 H633 R634
BS03	dna	B	T287 A573 Y574 S596 R598 G599 Q600 S627 S630	T257 A543 Y544 S566 R568 G569 Q570 S597 S600

External links

• PDB: RCSB:9ezy, PDBe:9ezy, PDBj:9ezy
• PDBsum: 9ezy
• PubMed: 38870273
• UniProt: Q9KR73