Structure of PDB 5gjp Chain A Binding Site BS02

Receptor Information
>5gjp Chain A (length=381) Species: 971 (Selenomonas ruminantium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKNFRLSEKEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAM
KANPTPEILSLLAGLGSHFDVASAGEMEILHELGVDGSQMIYANPVKDAR
GLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLVRIAVRNTKFGAPVEE
ALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALLVARRLFDEAEEMG
MHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRLFPDTAVWTEPGR
YMCGTAVNLVTSVIGTKTRGEQPWYILDEGIYGCFSGIMYDHWTYPLHCF
GKGNKKPSTFGGPSCDGIDVLYRDFMAPELKIGDKVLVTEMGSYTSVSAT
RFNGFYLAPTIIFEDQPEYAARLTEDDDVKK
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 chain5gjp Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5gjp Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium
Resolution2.5 Å
Binding residue
(original residue number in PDB)		A49 K51 H179 S182 G219 E255 G257 R258 Y352
Binding residue
(residue number reindexed from 1)		A49 K51 H171 S174 G211 E247 G249 R250 Y344
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K51 H179 E255
Catalytic site (residue number reindexed from 1) K51 H171 E247
Enzyme Commision number 4.1.1.17: ornithine decarboxylase.
4.1.1.18: lysine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004586 ornithine decarboxylase activity
GO:0008923 lysine decarboxylase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0008295 spermidine biosynthetic process
GO:0009446 putrescine biosynthetic process
GO:0033387 putrescine biosynthetic process from ornithine
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5gjp, PDBe:5gjp, PDBj:5gjp
PDBsum5gjp
PubMed27861532
UniProtO50657|DCLO_SELRU Lysine/ornithine decarboxylase (Gene Name=ldc)

[Back to BioLiP]