Structure of PDB 4bmk Chain B

Receptor sequence

>4bmkB (length=386) Species: 13689 (Sphingomonas paucimobilis)

RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLG
TYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRD
FYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNA
EIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVA
KKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSASVGTVG
GFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRER
LWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGG
LYVNMALLRCSICAEHTPAQIQTVLGMFQAAGRAVG

3D structure

• PDB: 4bmk The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin.
• Chain: B
• Resolution: 1.62 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y73 H159 E202 S206 D231 H234 A265
• Catalytic site (residue number reindexed from 1): Y52 H138 E181 S185 D210 H213 A244
• Enzyme Commision number: 2.3.1.50: serine C-palmitoyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	PLP	B	T294 A295	T273 A274
BS02	MYB	B	L105 F293 T294	L84 F272 T273
BS03	PLP	B	G134 Y135 H159 E202 D231 H234 T262 S264	G113 Y114 H138 E181 D210 H213 T241 S243
BS04	MYB	B	Y73 H159	Y52 H138

Gene Ontology

Molecular Function

• GO:0016746 acyltransferase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0006629 lipid metabolic process
• GO:0006665 sphingolipid metabolic process
• GO:0009058 biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4bmk, PDBe:4bmk, PDBj:4bmk
• PDBsum: 4bmk
• PubMed: 23957439
• UniProt: Q93UV0|SPT_SPHPI Serine palmitoyltransferase (Gene Name=spt)