SMTL ID : 3rlh.1

Crystal structure of a class II phospholipase D from Loxosceles intermedia venom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: E.81, D.83, D.141, K.143 Ligands: PEG.4, PEG.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.81, A:D.83, A:D.141, H2O.1

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: N.89, D.154, K.157, K.158, K.161, Q.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.158

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: N.187, Y.189, A.227, K.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.230 PEG.4: 9 residues within 4Å: Chain A: H.61, E.81, D.83, H.97, D.141, K.143, M.294 Ligands: MG.1, PEG.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.97, A:K.143 Water bridges: A:S.216, A:S.216, A:Y.272 PEG.5: 1 residues within 4Å: Chain A: K.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.311 Water bridges: A:K.311 PEG.6: 9 residues within 4Å: Chain A: H.61, H.97, D.141, K.143, Y.272, W.274, M.294 Ligands: MG.1, PEG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.61, A:Y.272, A:Y.272 Water bridges: A:K.143, A:K.143

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: E.71, F.72, L.75, R.105, N.296, Y.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.71, A:E.71 EDO.8: 3 residues within 4Å: Chain A: S.146, L.147, Y.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Giuseppe, P.O. et al., Structure of a novel class II phospholipase D: Catalytic cleft is modified by a disulphide bridge. Biochem.Biophys.Res.Commun. (2011)

Release Date

2011-06-29

Peptides

Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a