Structure of PDB 6n2f Chain B Binding Site BS01

Receptor Information
>6n2f Chain B (length=421) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDHCFKKSSDGFLYCEGTKVQDIMETVEKRPFYLYSKPQITRNLEAYKEA
LEGVRSVIGYAIKANNNLKILEHLRSLGCGAVLVSGNELRLALLAGFDPT
KCIFNGNGKSLEDLVLAAQEGVFVNVDSEFDLNNIVEASRISGKQVNVLL
RINPDVDQVHPYVATGNKNSKFGIRNEKLQWFLDEVKAHPKELKLVGAHC
HLGSTITKVDIFRDAAVLMIEYIDEIRRQGFEVSYLNIGGGLGIDYYHAG
AVLPTPMDLINTVRELVLSRDLNLIIEPGRSLIANTCCFVNHVTGVKTNG
TKNFIVIDGSMAELIRPSLYDAYQHIELVSPTPPEAEVTKFDVVGPVCES
ADFLGKDRELPTPPQGAGLVVHDAGAYCMSMASTYNLKMRPPEYWVEEDG
SITKIRHAETFDDHLRFFEGL
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 chain6n2f 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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PDB6n2f Active site gating provides stereochemical control for meso-diaminopimelate decarboxylase
Resolution2.27 Å
Binding residue
(original residue number in PDB)		K81 H220 S223 G260 E296 G298 R299 Y396
Binding residue
(residue number reindexed from 1)		K63 H201 S204 G241 E277 G279 R280 Y377
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:6n2f, PDBe:6n2f, PDBj:6n2f
PDBsum6n2f
PubMed
UniProtQ94A94|DCDA2_ARATH Diaminopimelate decarboxylase 2, chloroplastic (Gene Name=LYSA2)

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