2025-09-06_00000038|ligand|9DIE

Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution; X-ray diffraction 1.85Å

Protein #1 301 residues (92% resolved)

Raw Sequence ...

MKHHHHHHHHGGLVPRGSHGGSGDSRRPIWNIAHMVNDLDLVDEYLDDGANSLELDVEFSKSGTALRTYNGVPCDCFRSCTRSEKFSKYLDYIRQLTTPGNSKFRSRLILLVLDLKLNPLSSSAAYNAGADVARNLLDNYWQRGDSKARAYIVLSLETIAGAEFITGFKDTMKKEGFDEKYYDKIGWDFSGNEDLGKIRDVLESHGIREHIWQGDGITNCLPRDDNRLKQAISRRYSPTYVYADKVYTWSIDKESSIENALRLGVDGVMTNYPARVISVLGEREFSGKLRLATYDDNPWEK

Canonical Sequence ...

Non polymer #2 A1A43

InChI=1S/C31H63N2O6P/c1-3-5-7-9-11-13-14-15-17-18-20-22-24-30(34)29(28-39-40(36,37)38-27-26-32)33-31(35)25-23-21-19-16-12-10-8-6-4-2/h22,24,29-30,34H,3-21,23,25-28,32H2,1-2H3,(H,33,35)(H,36,37)/b24-22+/t29-,30+/m0/s1

InChI=1S/C31H63N2O6P/c1-3-5-7-9-11-13-14-15-17-18-20-22-24-30(34)29(28-39-40(36,37)38-27-26-32)33-31(35)25-23-21-19-16-12-10-8-6-4-2/h22,24,29-30,34H,3-21,23,25-28,32H2,1-2H3,(H,33,35)(H,36,37)/b24-22+/t29-,30+/m0/s1

SMILES: CCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)(O)OCCN)NC(=O)CCCCCCCCCCC)O

CCCCCCCCCCCC/C=C/[C@H]([C@H](COP(=O)(O)OCCN)NC(=O)CCCCCCCCCCC)O

Non polymer #3 A1A44

InChI=1S/C29H56NO5P/c1-3-5-7-9-11-13-14-15-17-18-20-22-24-28-27(26-34-36(32,33)35-28)30-29(31)25-23-21-19-16-12-10-8-6-4-2/h22,24,27-28H,3-21,23,25-26H2,1-2H3,(H,30,31)(H,32,33)/b24-22+/t27-,28+/m0/s1

InChI=1S/C29H56NO5P/c1-3-5-7-9-11-13-14-15-17-18-20-22-24-28-27(26-34-36(32,33)35-28)30-29(31)25-23-21-19-16-12-10-8-6-4-2/h22,24,27-28H,3-21,23,25-26H2,1-2H3,(H,30,31)(H,32,33)/b24-22+/t27-,28+/m0/s1

SMILES: CCCCCCCCCCCC/C=C/[C@@H]1[C@H](COP(=O)(O1)O)NC(=O)CCCCCCCCCCC

CCCCCCCCCCCC/C=C/[C@@H]1[C@H](COP(=O)(O1)O)NC(=O)CCCCCCCCCCC

Non polymer #4 MG

InChI=1S/Mg/q+2

SMILES: [Mg+2]

[Mg+2]

Non polymer #5 MPD

InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1

SMILES: C[C@@H](CC(C)(C)O)O

C[C@@H](CC(C)(C)O)O

Non polymer #6 NA

InChI=1S/Na/q+1

SMILES: [Na+]

[Na+]

Biounit #1 monomer

Biounit #2 monomer

Reference