Structure of PDB 8d4i Chain C Binding Site BS01

Receptor Information
>8d4i Chain C (length=462) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTDSIMQNYNQLREQVINGDRRFQHKDGHLCFEGVDLDALARQYPTPFYV
FSEPEIIRNIHEIQQAFAAHKNTKTFFASKTCSVMGVLKAIRDAGICAEA
NSQYEVRKCLEIGFRGDQIVFNGVVKKPADLEYAIANDLYLINVDSLYEL
EHIDAISRKLKKVANVCVRVEPNVPSLVTAFHAKSGLDLEQAEETCRRIL
AMPYVHLRGLHMHVGDQVPESEPFAKATKVLVDESRRLEEVLGIKFDLIN
VGGGIPVPYKYDDENGDPLKDNMYAGITAQDFADAVIREVHKWRTDVEIC
IEPGRKVTGSAAVLLTEVSCEKRKTNYDLNGNVECHVEWKFVDAGYSVLS
DSQHFDWFFYVYNASRMTAAHDAWIKLAGPLCDGGDYFHMGVKGEEFLLP
KETHVGDIVAFLDAGAYTIESQTVFNNRPRTGVVMIDKNGDTRLIRREDS
YEDMVKYDIYLA
Ligand information
Ligand IDPUT
InChIInChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2
InChIKeyKIDHWZJUCRJVML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CCN)CN
ACDLabs 10.04
CACTVS 3.341		NCCCCN
FormulaC4 H12 N2
Name1,4-DIAMINOBUTANE;
PUTRESCINE
ChEMBLCHEMBL46257
DrugBankDB01917
ZINCZINC000005828633
PDB chain8d4i Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8d4i The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Resolution1.32 Å
Binding residue
(original residue number in PDB)		Q358 D361
Binding residue
(residue number reindexed from 1)		Q353 D356
Annotation score5
Enzymatic activity
Enzyme Commision number 4.1.1.116: D-ornithine/D-lysine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008836 diaminopimelate decarboxylase activity
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0009089 lysine biosynthetic process via diaminopimelate

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Molecular Function
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Biological Process
External links
PDB RCSB:8d4i, PDBe:8d4i, PDBj:8d4i
PDBsum8d4i
PubMed36265649
UniProtQ8ZNC4|DOKDC_SALTY D-ornithine/D-lysine decarboxylase (Gene Name=dokD)

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