Structure of PDB 6n2a Chain B Binding Site BS02

Receptor Information
>6n2a Chain B (length=411) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDHCFKKSSDGFLYCEGTKVEDIMESVERRPFYLYSKPQITRNLEAYKEA
LEGVSSVIGYAIKANNNLKILEHLRSLGCGAVLVSGNELRLALRAGFDPT
KCIFNGNGKSLEDLVLAAQEGVFVNVDSEFDLNNIVEASRISGKQVNVLL
RINPDGNKNSKFGIRNEKLQWFLDQVKAHPKELKLVGAHCHLGSTITKVD
IFRDAAVLMIEYIDEIRRQGFEVSYLNIGGGLGIDYYHAGAVLPTPMDLI
NTVRELVLSRDLNLIIEPGRSLIANTCCFVNHVTGVKTNGTKNFIVIDGS
MAELIRPSLYDAYQHIELVSPPPAEAEVTKFDVVGPVCESADFLGKDREL
PTPPQGAGLVVHDAGAYCMSMASTYNLKMRPPEYWVEEDGSITKIRHAET
FDDHLRFFEGL
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 chain6n2a Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6n2a Active site gating provides stereochemical control for meso-diaminopimelate decarboxylase
Resolution1.88 Å
Binding residue
(original residue number in PDB)		K77 H216 S219 G256 E292 G294 R295 Y392
Binding residue
(residue number reindexed from 1)		K63 H191 S194 G231 E267 G269 R270 Y367
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
Biological Process
GO:0009089 lysine biosynthetic process via diaminopimelate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6n2a, PDBe:6n2a, PDBj:6n2a
PDBsum6n2a
PubMed
UniProtQ949X7|DCDA1_ARATH Diaminopimelate decarboxylase 1, chloroplastic (Gene Name=LYSA1)

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