Structure of PDB 2qgh Chain A Binding Site BS01

Receptor Information
>2qgh Chain A (length=394) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLS
ILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALK
LNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYISTGL
KENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDLEPIIEASQK
VAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL
DLTIICEPGRSIVAESGELITQVLYEKKNKRFVIVDAGMNDFLRPSLYHA
KHAIRVITPSEISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGA
YGSSMASQYNSRPKLLELALEDKIRVIRKREALEDLWRLEEEGL
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 chain2qgh Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2qgh Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K46 D65 H185 S188 G224 G225 E259 P260 G261 R262 Y358
Binding residue
(residue number reindexed from 1)		K44 D63 H183 S186 G222 G223 E257 P258 G259 R260 Y351
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K46 H185 E259
Catalytic site (residue number reindexed from 1) K44 H183 E257
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:2qgh, PDBe:2qgh, PDBj:2qgh
PDBsum2qgh
PubMed
UniProtB4XMC6|DCDA_HELPX Diaminopimelate decarboxylase (Gene Name=lysA)

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