Structure of PDB 7kdy Chain B Binding Site BS03

Receptor Information
>7kdy Chain B (length=664) Species: 2689386 (Streptomyces tokunonensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRKVYFVGLNEYPFLPLVAGLLRTYAEQDERIAAAYDFQEPVFLVAPVQE
MADGIVEPDVLALSCYVWNFRRQMKVAKLVKERYPNVLVVAGGPHVPDRP
GNFFEKHPYVDVLAHGEGEVAFRELLATRLSDHPDYTAVPGVSVRRGTEA
VVGPKAKRLPRLIDTPSPYLLGVMDGAVATCRERGLRFYALWETNRGCPY
SCSFCDWGSATMSTLRKFEDERLQDEIEWFARHDVEDLFICDANFGIMPR
DLEIAHALAEARGELGAPRQVRVNFAKNSNDRVFDISKTWHDADLLMGTT
LSMQSTDMDVLEAIDRKNIGLDNYRKLQQRYAAENIHTYTELILGLPMET
ARSFRDGIGSLLEAGNHEDLRVYELGILPNAPLNTPEKIEQYGLRTVPKR
MYVERPGTPDDEAETFEMVMETNAMPRDAWVESFSFIQAVQFLHNGCYTR
YLSIFLRQEHGIGYTRFYEGLQDYFTGRPDTVLGALYLRMRSLYHDYIDM
PALPLANLVASQPDMAADLAPYGRRRGWTIDNWGWLRIATDFDRFHTELR
EYLATLGLDPAGDARLEDVLRFQQDVMLRPDYSPELGKSAEYAHDWPGYF
AGGLLRPRRVRVAYGDQSFGANGRYRPVPGDLKAFTMAAIGTSYPVSRMG
HFCHRFESAEVTSL
Ligand information
Ligand IDMET
InChIInChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
InChIKeyFFEARJCKVFRZRR-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CSCC[CH](N)C(O)=O
OpenEye OEToolkits 1.5.0CSCCC(C(=O)O)N
CACTVS 3.341CSCC[C@H](N)C(O)=O
OpenEye OEToolkits 1.5.0CSCC[C@@H](C(=O)O)N
ACDLabs 10.04O=C(O)C(N)CCSC
FormulaC5 H11 N O2 S
NameMETHIONINE
ChEMBLCHEMBL42336
DrugBankDB00134
ZINCZINC000001532529
PDB chain7kdy Chain B Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7kdy Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
Resolution1.939 Å
Binding residue
(original residue number in PDB)		W215 A251 N252 N282 F283 K285 R324
Binding residue
(residue number reindexed from 1)		W207 A243 N244 N274 F275 K277 R316
Annotation score4
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7kdy, PDBe:7kdy, PDBj:7kdy
PDBsum7kdy
PubMed35110734
UniProtA0A6B9HEI0

[Back to BioLiP]