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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

7YJ1

Cryo-EM structure of SPT-ORMDL3 (ORMDL3-deltaN2) complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0009058biological_processbiosynthetic process
A0030170molecular_functionpyridoxal phosphate binding
B0004758molecular_functionserine C-palmitoyltransferase activity
B0005515molecular_functionprotein binding
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0006629biological_processlipid metabolic process
B0006665biological_processsphingolipid metabolic process
B0006686biological_processsphingomyelin biosynthetic process
B0009058biological_processbiosynthetic process
B0016020cellular_componentmembrane
B0016740molecular_functiontransferase activity
B0016746molecular_functionacyltransferase activity
B0017059cellular_componentserine palmitoyltransferase complex
B0030148biological_processsphingolipid biosynthetic process
B0030170molecular_functionpyridoxal phosphate binding
B0046511biological_processsphinganine biosynthetic process
B0046512biological_processsphingosine biosynthetic process
B0046513biological_processceramide biosynthetic process
B0060612biological_processadipose tissue development
B1904504biological_processpositive regulation of lipophagy
C0004758molecular_functionserine C-palmitoyltransferase activity
C0005515molecular_functionprotein binding
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0006629biological_processlipid metabolic process
C0006665biological_processsphingolipid metabolic process
C0008104biological_processprotein localization
C0016020cellular_componentmembrane
C0017059cellular_componentserine palmitoyltransferase complex
C0030148biological_processsphingolipid biosynthetic process
C0046512biological_processsphingosine biosynthetic process
C0046513biological_processceramide biosynthetic process
D0002903biological_processnegative regulation of B cell apoptotic process
D0005515molecular_functionprotein binding
D0005783cellular_componentendoplasmic reticulum
D0005789cellular_componentendoplasmic reticulum membrane
D0005886cellular_componentplasma membrane
D0006665biological_processsphingolipid metabolic process
D0006672biological_processceramide metabolic process
D0006686biological_processsphingomyelin biosynthetic process
D0006940biological_processregulation of smooth muscle contraction
D0010508biological_processpositive regulation of autophagy
D0016020cellular_componentmembrane
D0017059cellular_componentserine palmitoyltransferase complex
D0030148biological_processsphingolipid biosynthetic process
D0030667cellular_componentsecretory granule membrane
D0035579cellular_componentspecific granule membrane
D0042552biological_processmyelination
D0061744biological_processmotor behavior
D0090153biological_processregulation of sphingolipid biosynthetic process
D0090156biological_processintracellular sphingolipid homeostasis
D1900060biological_processnegative regulation of ceramide biosynthetic process
D1900182biological_processpositive regulation of protein localization to nucleus
D2000303biological_processregulation of ceramide biosynthetic process
Functional Information from PROSITE/UniProt
site_idPS00599
Number of Residues10
DetailsAA_TRANSFER_CLASS_2 Aminotransferases class-II pyridoxal-phosphate attachment site. TFTKSFGASG
ChainResidueDetails
BTHR376-GLY385
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues56
DetailsTransmembrane: {"description":"Helical","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues1
DetailsModified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues73
DetailsTransmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"33558762","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6M4N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6M4O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7CQI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7CQK","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues49
DetailsTopological domain: {"description":"Cytoplasmic","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues7
DetailsTopological domain: {"description":"Lumenal","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsModified residue: {"description":"Hydroxyproline","evidences":[{"source":"PubMed","id":"36408842","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues1
DetailsSite: {"description":"Within the serine palmitoyltransferase (SPT) complex, defines the length of the acyl chain-binding pocket, determining the acyl-CoA substrate preference"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues1
DetailsModified residue: {"description":"Phosphotyrosine; by ABL","evidences":[{"source":"PubMed","id":"23629659","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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