SMTL ID : 3rlg.1

Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.54, D.56, D.114, K.116 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:D.56, A:D.114, H2O.3, H2O.7

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

EDO.2: 2 residues within 4Å: Chain A: N.218, K.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.251 EDO.5: 5 residues within 4Å: Chain A: L.159, N.160, D.196, A.200, K.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.196 EDO.6: 4 residues within 4Å: Chain A: D.61, N.62, Y.121, Q.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.62 EDO.9: 6 residues within 4Å: Chain A: G.198, Y.201, K.202, I.206, T.207, F.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.198, A:I.206

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

PEG.3: 2 residues within 4Å: Chain A: K.131 Ligands: PGE.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.62 PEG.8: 2 residues within 4Å: Chain A: K.284 Ligands: PGE.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.284

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

PGE.4: 7 residues within 4Å: Chain A: N.62, D.127, K.130, K.131, K.134, Q.171 Ligands: PEG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.131 PGE.7: 3 residues within 4Å: Chain A: A.281, K.285 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ullah, A. et al., Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom. Acta Crystallogr.,Sect.F (2011)

Release Date

2011-08-24

Peptides

Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase D LiSicTox-alphaIA1a

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