Structure of PDB 1v0u Chain A Binding Site BS01

Receptor Information

>1v0u Chain A (length=490) Species: 172564 (Streptomyces sp. PMF)

SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGC
WGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAG
LKESAAKGNKLKVRILVGAVIPSKYRDELTAKLGKAAENITLNVASMTTS
KTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAA
GSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPAT
GNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDY
DTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKM
AAGVKVRIVVSDPANRGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMC
SNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQD
FGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICN

Ligand information

• Ligand ID: PO3
• InChI: InChI=1S/O3P/c1-4(2)3/q-3
• InChIKey: AQSJGOWTSHOLKH-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [O-][P-]([O-])=O
  ACDLabs 10.04: [O-][PH2-]([O-])=O
  OpenEye OEToolkits 1.5.0: [O-][P-](=O)[O-]
• Formula: O3 P
• Name: PHOSPHITE ION
• PDB chain: 1v0u Chain A Residue 1515

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1v0u The Reaction Mechanism of Phospholipase D from Streptomyces Sp. Strain Pmf. Snapshots Along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product
• Resolution: 1.42 Å
• Binding residue (original residue number in PDB): H170 K172 H448 K450
• Binding residue (residue number reindexed from 1): H158 K160 H425 K427
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H170 D202 H448 D473
• Catalytic site (residue number reindexed from 1): H158 D190 H425 D450
• Enzyme Commision number: 3.1.4.4: phospholipase D.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004630 phospholipase D activity
• GO:0030572 phosphatidyltransferase activity

Biological Process

• GO:0032049 cardiolipin biosynthetic process

External links

• PDB: RCSB:1v0u, PDBe:1v0u, PDBj:1v0u
• PDBsum: 1v0u
• PubMed: 15165852
• UniProt: P84147