Structure of PDB 7yvs Chain F Binding Site BS02

Receptor Information

>7yvs Chain F (length=494) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EDLDTDNDNIPDSYERNGYTIKDLIAVKWEDSFAEQGYKKYVSNYLESNT
AGDPYTDYEKASGSFDKAIKTEARDPLVAAYPIVGVGMEKLIISTNEHAS
TDQGKTVSRATTNSKSTAVQDSNGESWNTGLSINKGESAYINANVRYYNT
GTAPMYKVTPTTNLVLDGDTLSTIKAQENQIGNNLSPGDTYPKKGLSPLA
LNTMDQFSSRLIPINYDQLKKLDAGKQIKLETTQVSGNFGTKNSSGQIVT
EGNSWSDYISQIDSISASIILDTENESYERRVTAKNLQDPEDKTPELTIG
EAIEKAFGATKKDGLLYFNDIPIDESCVELIFDDNTANKIKDSLKTLSDK
KIYNVKLERGMNILIKTPTYFTNFDDYNNYPSTWSNVNTTNQDGLQGSAN
KLNGETKIKIPMSELKPYKRYVFSGYSKDPLTSNSIIVKIKAKEEKTDYL
VPEQGYTKFSYEFETTEKDSSNIEITLIGSGTTYLDNLSITELN

Ligand information

Ligand ID

InChI

InChI=1S/Ca/q+2

InChIKey

BHPQYMZQTOCNFJ-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Ca++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Ca+2]

Formula

Name

CALCIUM ION

PDB chain

7yvs Chain F Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7yvs Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile.
Resolution	2.8 Å
Binding residue (original residue number in PDB)	D220 D222 D224 I226 E231
Binding residue (residue number reindexed from 1)	D4 D6 D8 I10 E15
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Biological Process
GO:0051260	protein homooligomerization

	Cellular Component
GO:0005576	extracellular region

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Biological Process

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Cellular Component

External links

PDB	RCSB:7yvs, PDBe:7yvs, PDBj:7yvs
PDBsum	7yvs
PubMed	36253419
UniProt	A8DS70

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