Structure of PDB 7kdx Chain B

Receptor sequence

>7kdxB (length=664) Species: 2689386 (Streptomyces tokunonensis)

SRGRKVYFVGLNEYPFLPLVAGLLRTYAEQDERIAAAYDFQEPVFLVAPV
QEMADGIVEPDVLALSCYVWNFRRQMKVAKLVKERYPNVLVVAGGPHVPD
RPGNFFEKHPYVDVLAHGEGEVAFRELLATRLSDHPDYTAVPGVSVRRGT
EAVVGPKAKRLPRLIDTPSPYLLGVMDGAVATCRERGLRFYALWETNRGC
PYSCSFCDWGSATMSTLRKFEDERLQDEIEWFARHDVEDLFICDANFGIM
PRDLEIAHALAEARGELGAPRQVRVNFAKNSNDRVFDISKTWHDADLLMG
TTLSMQSTDMDVLEAIDRKNIGLDNYRKLQQRYAAENIHTYTELILGLPM
ETARSFRDGIGSLLEAGNHEDLRVYELGILPNAPLNTPEKIEQYGLRTVP
KRMYVERTPDDEAETFEMVMETNAMPRDAWVESFSFIQAVQFLHNGCYTR
YLSIFLRQEHGIGYTRFYEGLQDYFTGRPDTVLGALYLRMRSLYHDYIDM
PALPLANLVASQPDMAADLAPYGRRRGWTIDNWGWLRIATDFDRFHTELR
EYLATLGLDPAGDARLEDVLRFQQDVMLRPDYSPELGKSAEYAHDWPGYF
AGGLLRPRRVRVAYGDQSFGANGRYRPVPGDLKAFTMAAIGTSYPVSRMG
HFCHRFESAEVTSL

3D structure

• PDB: 7kdx Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
• Chain: B
• Resolution: 1.791 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	B12	B	N18 F22 V26 L30 S72 Y74 V75 W76 G100 G101 P102 G124 E125 G126 E127 L199 D214 W215 G216 F247 C249 L386 Y652	N12 F16 V20 L24 S66 Y68 V69 W70 G94 G95 P96 G118 E119 G120 E121 L193 D208 W209 G210 F241 C243 L380 Y644
BS02	SF4	B	C206 Y208 C210 F212 C213 W215 R324	C200 Y202 C204 F206 C207 W209 R318
BS03	MET	B	W215 A251 N252 N282 F283 K285 R324	W209 A245 N246 N276 F277 K279 R318

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008168 methyltransferase activity
• GO:0031419 cobalamin binding
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0032259 methylation

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7kdx, PDBe:7kdx, PDBj:7kdx
• PDBsum: 7kdx
• PubMed: 35110734
• UniProt: A0A6B9HEI0