Structure of PDB 8ai5 Chain B

Receptor sequence

>8ai5B (length=323) Species: 1423 (Bacillus subtilis)

NLYFQGHMYNKTVSINLDSRCNASCDHCCFSSSPTSTTRMEKEYIRELVT
EFAKNKTIQVISFTGGEVFLDYKFLKELMEIIKPYEKQITLISNGFWGLS
KKKVQEYFHDMNSLNVIALTISYDEYHAPFVKSSSIKNILEHSRKYPDID
ISLNMAVTKDKMSNHILEELGDSILGVKITKFPMISVGAAKTRIKQENIH
KFYSLEDEDSLHCPGYDIVYHHDGEIYPCASPAIFETKITLREEYNQSFE
RTVEKLNSNLLLFILRKEGFKWFLNILKENNKIEEFDIPYEFSSICGVCG
SLFNSAEKINYFYPYMEKYYNEN

3D structure

• PDB: 8ai5 Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.
• Chain: B
• Resolution: 2.15 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	peptide	B	S7 T57 T83 A111 T113 D143 I144 S145 K171 F175 I178 P207 G208 D210 A223 S224 P225 F228 C289	S14 T64 T90 A118 T120 D150 I151 S152 K178 F182 I185 P214 G215 D217 A230 S231 P232 F235 C296
BS02	SF4	B	C14 A16 C18 C21 S25 G59 N87 H120	C21 A23 C25 C28 S32 G66 N94 H127
BS03	SF4	B	C206 C222 S224 F263 C289 C292	C213 C229 S231 F270 C296 C299
BS04	SAH	B	H20 C21 C22 G58 G59 I85 S115 H120 N147 F175 I178	H27 C28 C29 G65 G66 I92 S122 H127 N154 F182 I185

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:8ai5, PDBe:8ai5, PDBj:8ai5
• PDBsum: 8ai5
• PubMed: 38158457
• UniProt: Q45595|YYDG_BACSU Putative peptide biosynthesis protein YydG (Gene Name=yydG)