SMTL ID : 9die.2 (1 other biounit)

Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

2 x 01: 2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate

01.1: 13 residues within 4Å: Chain A: C.76, F.77, I.217, T.218, N.219, C.220, L.221, S.250, I.251, D.252, K.253, S.256 Ligands: 02.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.77 Hydrogen bonds: A:N.219, A:S.250, A:D.252, A:K.253, A:K.253, A:S.256, A:S.256 Water bridges: A:I.217, A:N.219 Salt bridges: A:K.253 01.2: 10 residues within 4Å: Chain A: L.41, Y.45, P.73, C.74, F.77, R.78, S.79, C.80, R.82 Ligands: 02.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.73, A:F.77, A:F.77 Hydrogen bonds: A:F.77, A:S.79 Water bridges: A:R.78, A:R.78, A:S.79, A:S.79 Salt bridges: A:R.78, A:R.82

1 x 02: N-{(2S,4R,5S)-2-hydroxy-2-oxo-4-[(1E,7Z)-tetradeca-1,7-dien-1-yl]-1,3,2lambda~5~-dioxaphosphinan-5-yl}dodecanamide

02.3: 16 residues within 4Å: Chain A: H.34, D.56, N.70, P.73, C.74, C.76, D.114, K.116, I.217, T.218, C.220, L.221, W.249 Ligands: 01.1, 01.2, MG.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.218, A:L.221 Hydrogen bonds: A:N.70, A:T.218 Water bridges: A:H.34, A:D.56 Salt bridges: A:H.34, A:K.116

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: D.114, S.155, L.156, E.157, S.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.155, A:S.190 NA.5: 4 residues within 4Å: Chain A: N.70, G.71, V.72, P.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.70 Water bridges: A:N.70, A:N.70

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: E.54, D.56, D.114, K.116 Ligands: 02.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:D.56, A:D.114, H2O.4, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundman, A.K. et al., Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution. To Be Published

Release Date

2025-09-10

Peptides

Dermonecrotic toxin StSicTox-betaIB1i: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dermonecrotic toxin StSicTox-betaIB1i

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