Structure of PDB 7kdy Chain B

Receptor sequence

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

GRKVYFVGLNEYPFLPLVAGLLRTYAEQDERIAAAYDFQEPVFLVAPVQE
MADGIVEPDVLALSCYVWNFRRQMKVAKLVKERYPNVLVVAGGPHVPDRP
GNFFEKHPYVDVLAHGEGEVAFRELLATRLSDHPDYTAVPGVSVRRGTEA
VVGPKAKRLPRLIDTPSPYLLGVMDGAVATCRERGLRFYALWETNRGCPY
SCSFCDWGSATMSTLRKFEDERLQDEIEWFARHDVEDLFICDANFGIMPR
DLEIAHALAEARGELGAPRQVRVNFAKNSNDRVFDISKTWHDADLLMGTT
LSMQSTDMDVLEAIDRKNIGLDNYRKLQQRYAAENIHTYTELILGLPMET
ARSFRDGIGSLLEAGNHEDLRVYELGILPNAPLNTPEKIEQYGLRTVPKR
MYVERPGTPDDEAETFEMVMETNAMPRDAWVESFSFIQAVQFLHNGCYTR
YLSIFLRQEHGIGYTRFYEGLQDYFTGRPDTVLGALYLRMRSLYHDYIDM
PALPLANLVASQPDMAADLAPYGRRRGWTIDNWGWLRIATDFDRFHTELR
EYLATLGLDPAGDARLEDVLRFQQDVMLRPDYSPELGKSAEYAHDWPGYF
AGGLLRPRRVRVAYGDQSFGANGRYRPVPGDLKAFTMAAIGTSYPVSRMG
HFCHRFESAEVTSL

3D structure

• PDB: 7kdy Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
• Chain: B
• Resolution: 1.939 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	SF4	B	C206 Y208 C210 F212 C213 W215 K285 R324	C198 Y200 C202 F204 C205 W207 K277 R316
BS02	B12	B	N18 F22 V26 L30 L71 S72 Y74 V75 W76 G100 G101 P102 G124 E125 G126 E127 L199 E201 D214 W215 G216 F247 C249 L386	N10 F14 V18 L22 L63 S64 Y66 V67 W68 G92 G93 P94 G116 E117 G118 E119 L191 E193 D206 W207 G208 F239 C241 L378
BS03	MET	B	W215 A251 N252 N282 F283 K285 R324	W207 A243 N244 N274 F275 K277 R316

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:7kdy, PDBe:7kdy, PDBj:7kdy
• PDBsum: 7kdy
• PubMed: 35110734
• UniProt: A0A6B9HEI0