Structure of PDB 7yjm Chain B Binding Site BS01

Receptor Information
>7yjm Chain B (length=471) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MITIPYLTAVSTYFSYGLLFAFGQLRDFFRRFIDWWLQGYAPICLGHEDF
YIRRLYHRIQDCFERPISSAPDAWFDVVERYSNDNNKTLKRTTKTSRCLN
LGSYNYLGFGSFDEYCTPRVIESLKKFSASTCSSRVDAGTTSVHAELEEC
VTRFVGKPAAVVFGMGYATNSAIIPVLIGKGGLIISDSLNHSSIVNGARG
SGATIRVFQHNTPSHLERVLREQIAEGQPRTHRPWKKIIVVVEGIYSMEG
EICHLPEVVAICKKYKAYVYLDEAHSIGAIGKTGKGICELLGVDTADVDV
MMGTFTKSFGSCGGYIAGSKELIQYLKHQCPAHLYATSIPTPSAQQIISA
IKVILGEDGSNRGAQKLARIRENSNFFRAELQKMGFEVLGDNDSPVMPIM
LYNPAKIPAFSRECLRQKVAVVVVGFPATPLLLARARICISASHSREDLI
RALKVISKVGDLSGIKYFPAE
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 chain7yjm 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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PDB7yjm Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G170 H195 D276 A278 H279 K311
Binding residue
(residue number reindexed from 1)		G166 H191 D272 A274 H275 K307
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.1.50: serine C-palmitoyltransferase.
Gene Ontology
Molecular Function
GO:0004758 serine C-palmitoyltransferase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006665 sphingolipid metabolic process
GO:0006915 apoptotic process
GO:0009058 biosynthetic process
GO:0009555 pollen development
GO:0009640 photomorphogenesis
GO:0043067 regulation of programmed cell death
GO:0046512 sphingosine biosynthetic process
Cellular Component
GO:0005773 vacuole
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7yjm, PDBe:7yjm, PDBj:7yjm
PDBsum7yjm
PubMed36989369
UniProtQ9LSZ9|LCB2A_ARATH Long chain base biosynthesis protein 2a (Gene Name=LCB2a)

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