Structure of PDB 6oq5 Chain A Binding Site BS01

Receptor Information

>6oq5 Chain A (length=2346) Species: 1496 (Clostridioides difficile)

SLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKD
INSLTDTYIDTYKKSGRNKALKKFKEYLVIEILELKNSNLTPVEKNLHFI
WIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTIIESASN
DTLESFRENLNDPEFNHTAFFRKRMQIIYDKQQNFINYYKAQKEENPDLI
IDDIVKTYLSNEYSKDIDELNAYIEESLNKVTENSGNDVRNFEEFKTGEV
FNLYEQELVERWNLAGASDILRVAILKNIGGVYLDVDMLPGIHPDLFKDI
NKPDSVKTAVDWEEMQLEAIMKHKEYIPEYTSKHFDTLDEEVQSSFESVL
ASKSDKSEIFLPLGDIEVSPLEVKIAFAKGSIINQALISAKDSYCSDLLI
KQIQNRYKILNDTLGPIISQGNDFNTTMNNFGESLGAIANEENISFIAKI
GSYLRVGFYPEANTTITLSGPTIYAGAYKDLLTFKEMSIDTSILSSELRN
FEFPKVNISQATEQEKNSLWQFNEERAKIQFEEYKKNYFEGALGEDDNLD
FSQNTVTDKEYLLEKISSSTKSSERGYVHYIVQLQGDKISYEAACNLFAK
NPYDSILFQKNIEDSEVAYYYNPTDSEIQEIDKYRIPDRISDRPKIKLTF
IGHGKAEFNTDIFAGLDVDSLSSEIETAIGLAKEDISPKSIEINLLGCNM
FSYSVNVEETYPGKLLLRVKDKVSELMPSMSQDSIIVSANQYEVRINSEG
RRELLDHSGEWINKEESIIKDISSKEYISFNPKENKIIVKSKNLPELSTL
LQEIRNNSNSSDIELEEKVMLAECEINVISNIETQVVEERIEEAKSLTSD
SINYIKNEFKLIESISDALCDLKQQNELEDSHFISFEDISETDEGFSIRF
INKETGESIFVETEKTIFSEYANHITEEISKIKGTIFDTVNGNLDTTHEV
NTLNAAFFIQSLIEYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAK
VVELVSTALDETIDLLPTLSEGLPELSETSDPLLRQEIEAKIGIMAVNLT
TATTAIITSSLGIASGFSILLVPLAGISAGIPSLVNNELVLRDKATKVVD
YFKHVSLVETEGVFTLLDDKVMMPQDDLVISEIDFNNNSIVLGKCEIWRM
EGGSGHTVTDDIDHFFSAPSITYREPHLSIYDVLEVQKEELDLSKDLMVL
PNAPNRVFAWETGWTPGLRSLENDGTKLLDRIRDNYEGEFYWRYFAFIAD
ALITTLKPRYEDTNIRINLDSNTRSFIVPIITTEYIREKLSYSFYGSGGT
YALSLSQYNMGINIELSESDVWIIDVDNVVRDVTIESDKIKKGDLIEGIL
STLSIEENKIILNSHEINFSGEVNGSNGFVSLTFSILEGINAIIEVDLLS
KSYKLLISGELKILMLNSNHIQQKIDYIGFNSELQKNIPYSFVDSEGKEN
GFINGSTKEGLFVSELPDVVLISKVYMDDSKPSFGYYSNNLKDVKVITKD
NVNILTGYYLKDDIKISLSLTLQDEKTIKLNSVHLDESGVAEILKFMNRK
GSTNTSDSLMSFLESMNIKSIFVNFLQSNIKFILDANFIISGTTSIGQFE
FICDENNNIQPYFIKFNTLETNYTLYVGNRQNMIVEPNYDLDDSGDISST
VINFSQKYLYGIDSCVNKVVISPNIYTDEINITPVYETNNTYPEVIVLDA
NYINEKINVNINDLSIRYVWSNDGNDFILMSTSEENKVSQVKIRFVNVFK
DKTLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYDLGLVSLYNEK
FYINNFGMMVSGLIYINDSLYYFKPPVNNLITGFVTVGDDKYYFNPINGG
AASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENLEGEA
IDFTGKLIIDENIYYFEDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQI
GDDKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAEN
GEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDS
FTAVVGWKDLEDGSKYYFDEDTAEAYIGLSLINDGQYYFNDDGIMQVGFV
TINDKVFYFSDSGIIESGVQNIDDNYFYIDDNGIVQIGVFDTSDGYKYFA
PANTVNDNIYGQAVEYSGLVRVGEDVYYFGETYTIETGWIYDMENESDKY
YFDPETKKACKGINLIDDIKYYFDEKGIMRTGLISFENNNYYFNENGEMQ
FGYINIEDKMFYFGEDGVMQIGVFNTPDGFKYFAHQNTLDENFEGESINY
TGWLDLDEKRYYFTDEYIAATGSVIIDGEEYYFDPDTAQLVISEHH

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 6oq5 Chain A Residue 2801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6oq5 Structure of the full-length Clostridium difficile toxin B.
• Resolution: 3.87 Å
• Binding residue (original residue number in PDB): D547 H654 C699 H758
• Binding residue (residue number reindexed from 1): D546 H653 C698 H757
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008234 cysteine-type peptidase activity
• GO:0008289 lipid binding
• GO:0016757 glycosyltransferase activity
• GO:0046872 metal ion binding
• GO:0090729 toxin activity

Biological Process

• GO:0006508 proteolysis
• GO:0035821 modulation of process of another organism

Cellular Component

• GO:0005576 extracellular region
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0020002 host cell plasma membrane
• GO:0030430 host cell cytoplasm
• GO:0044164 host cell cytosol
• GO:0044174 host cell endosome
• GO:0044175 host cell endosome membrane

External links

• PDB: RCSB:6oq5, PDBe:6oq5, PDBj:6oq5
• PDBsum: 6oq5
• PubMed: 31308519
• UniProt: M4NKV9