Structure of PDB 8y9b Chain B

Receptor sequence

>8y9bB (length=1607) Species: 1496 (Clostridioides difficile)

SLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKD
INSLTDIYIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFV
WIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAIN
DTLESFRENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELI
IDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFEEFKNGES
FNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESI
EKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLA
SKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVK
QIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELG
KYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNF
EISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSLGEDDNLDF
SQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKT
PYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFI
GHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMF
SYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGR
RELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNLPELSTLL
QEIRNNSNSSDIELEEKVMLTECEINVISNIDTQIVEERIEEAKNLTSDS
INYIKDEFKLIESISDALCDLKQQNELEDSHFISFEDISETDEGFSIRFI
NKETGESIFVETEKTIFSEYANHITEEISKIKGTIFDTVNGKLVKKVNAA
FFIQSLIEYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVS
TALDETIDLLPTLSKLSYSFYGSGGTYALSLSQYNMGINIELSESDVWII
DVDNVVRDVTIKKGDLIEGILSTLSIEENKIILNSHEINFSGEVNGSNGF
VSLTFSILEGINAIIEVDLLSKSYKLLISGELKILMLNSNHIQQKIDYIG
FNSELQKNIPYSFVDSEGKENGFINGSTKEGLFVSELPDVVLISKVYMDD
SKPSFGYYSNNLKDVKVITKDNVNILTGYYLKDDIKISLSLTLQDEKTIK
LNSVHLDESGVAEILKFMNRKGDSLMSFLESMNIKSIFVNFLQSNIKFIL
DANFIISGTTSIGQFEFICDENDNIQPYFIKFNTLETNYTLYVGNRQNMI
VEPNYDLDDSGDISSTVINFSQKYLYGIDSCVNKVVISPNIYTDEINITP
VYETNNTYPEVIVLDANYINEKINVNINDLSIRYVWSNDGNDFILMSTSE
ENKVSQVKIRFVNVFKDKTLANKLSFNFSDKQDVPVSEIILSFTPSYYED
GLIGYDLGLVSLYNEKFYINNFGMMVSGLIYINDSLYYFKPPVNNLITGF
VTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFK
YFAPANT

3D structure

• PDB: 8y9b TcdB1 in complex with mini-binder
• Chain: B
• Resolution: 3.2 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	ZN	B	D546 H653 C698 H757	D545 H652 C697 H756

External links

• PDB: RCSB:8y9b, PDBe:8y9b, PDBj:8y9b
• PDBsum: 8y9b
• UniProt: P18177|TCDB_CLODI Toxin B (Gene Name=tcdB)