Structure of PDB 5x7m Chain A Binding Site BS01

Receptor Information
>5x7m Chain A (length=443) Species: 196627 (Corynebacterium glutamicum ATCC 13032) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVENFNELPAHVWPRNAVRQEDGVVTVAGVPLPDLAEEYGTPLFVVDEDD
FRSRCRDMATAFGGPGNVHYASKAFLTKTIARWVDEEGLALDIASINELG
IALAAGFPASRITAHGNNKGVEFLRALVQNGVGHVVLDSAQELELLDYVA
AGEGKIQDVLIRVKPGIEAHTHEFIATSHEDQKFGFSLASGSAFEAAKAA
NNAENLNLVGLHCHVGSQVFDAEGFKLAAERVLGLYSQIHSELGVALPEL
DLGGGYGIAYTAAEEPLNVAEVASDLLTAVGKMAAELGIDAPTVLVEPGR
AIAGPSTVTIYEVGTTKDVHVDDDKTRRYIAVDGGMSDNIRPALYGSEYD
ARVVSRFAEGDPVSTRIVGSHCESGDILINDEIYPSDITSGDFLALAATG
AYCYAMSSRYNAFTRPAVVSVRAGSSRLMLRRETLDDILSLEA
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain5x7m Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5x7m Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		K75 H117 H216 G256 G257 E299 G301 R302 Y404
Binding residue
(residue number reindexed from 1)		K73 H115 H214 G254 G255 E297 G299 R300 Y402
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.20: diaminopimelate 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
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5x7m, PDBe:5x7m, PDBj:5x7m
PDBsum5x7m
PubMed29233695
UniProtP09890|DCDA_CORGL Diaminopimelate decarboxylase (Gene Name=lysA)

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