Structure of PDB 2yxx Chain A Binding Site BS01

Receptor Information
>2yxx Chain A (length=385) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DILRKVAEIHGTPTYVYFEETLRKRSRLVKEVFEGVNLLPTFAVKANNNP
VLLKILREEGFGMDVVTKGELLAAKLAGVPSHTVVWNGNGKSRDQMEHFL
REDVRIVNVDSFEEMEIWRELNPEGVEYFIRVNPEVDAKTHPHISTGLKK
HKFGIPLEDLDSFMERFRSMNIRGLHVHIGSQITRVEPFVEAFSKVVRAS
ERYGFEEINIGGGWGINYSGEELDLSSYREKVVPDLKRFKRVIVEIGRYI
VAPSGYLLLRVVLVKRRHNKAFVVVDGGMNVLIRPALYSAYHRIFVLGKQ
GKEMRADVVGPLCESGDVIAYDRELPEVEPGDIIAVENAGAYGYTMSNNY
NSTTRPAEVLVRENGRISLIRRRETEMDIFKDVVM
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 chain2yxx Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yxx Crystal structure analysis of Diaminopimelate decarboxylate (lysA)
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K46 D65 H179 S182 G214 E246 G248 R249 Y343
Binding residue
(residue number reindexed from 1)		K45 D64 H178 S181 G213 E245 G247 R248 Y342
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K46 H179 E246
Catalytic site (residue number reindexed from 1) K45 H178 E245
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:2yxx, PDBe:2yxx, PDBj:2yxx
PDBsum2yxx
PubMed
UniProtQ9X1K5|DCDA_THEMA Diaminopimelate decarboxylase (Gene Name=lysA)

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