Structure of PDB 3mad Chain A Binding Site BS01

Receptor Information

>3mad Chain A (length=451) Species: 2734 (Symbiobacterium thermophilum)

KPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHG
DEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAG
GTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKA
AQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGYPHGVVDPI
PEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSA
DTHKYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGLYFSPTFAGSRPGA
LSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWV
IAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRF
LADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVLTGFIDLLYEV
H

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 3mad Chain A Residue 514

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mad Structure and Function of Sphingosine-1-Phosphate Lyase, a Key Enzyme of Sphingolipid Metabolism.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): A103 Y105
• Binding residue (residue number reindexed from 1): A46 Y48
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 4.1.2.27: sphinganine-1-phosphate aldolase.

Gene Ontology

Molecular Function

• GO:0004058 aromatic-L-amino-acid decarboxylase activity
• GO:0008117 sphinganine-1-phosphate aldolase activity
• GO:0016829 lyase activity
• GO:0016830 carbon-carbon lyase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0042802 identical protein binding

Biological Process

• GO:0019752 carboxylic acid metabolic process
• GO:0030149 sphingolipid catabolic process

External links

• PDB: RCSB:3mad, PDBe:3mad, PDBj:3mad
• PDBsum: 3mad
• PubMed: 20696404
• UniProt: Q67PY4