Structure of PDB 7yjm Chain B Binding Site BS02

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 IDZ1T
InChIInChI=1S/C42H83NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,40-41,44-45H,3-34,36,38-39H2,1-2H3,(H,43,46)/b37-35+/t40-,41+/m0/s1
InChIKeyZJVVOYPTFQEGPH-AUTSUKAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](C=CCCCCCCCCCCCCC)O
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC
ACDLabs 12.01O=C(NC(CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCCCCCCCCCCCCCCCCCCCC
CACTVS 3.370CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[CH](CO)[CH](O)C=CCCCCCCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(CO)C(C=CCCCCCCCCCCCCC)O
FormulaC42 H83 N O3
NameN-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide
ChEMBL
DrugBank
ZINCZINC000040164306
PDB chain7yjm Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		Y13 F20 Y55
Binding residue
(residue number reindexed from 1)		Y13 F20 Y51
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

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Molecular Function
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Biological Process
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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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