SMTL ID : 4rw5.1

Structural insights into substrate binding of brown spider venom class II phospholipases D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 6 residues within 4Å: Chain A: N.62, D.127, K.130, K.131, K.134, Q.171 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.130, A:K.131, A:K.134 Water bridges: A:N.62 Salt bridges: A:K.131

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.61, Y.121, N.123, Q.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.61, A:N.123

1 x TDA: N-TRIDECANOIC ACID(Non-covalent)

TDA.4: 3 residues within 4Å: Chain A: N.160, Y.162, K.203 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.162 Salt bridges: A:K.203

1 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.5: 12 residues within 4Å: Chain A: E.54, D.56, H.70, D.114, K.116, S.155, D.187, S.189, Y.245, W.247, M.267 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.114, A:W.247, A:W.247 Salt bridges: A:H.70, A:K.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coronado, M.A. et al., Structural Insights into Substrate Binding of Brown Spider Venom Class II Phospholipases D. Curr Protein Pept Sci (2015)

Release Date

2015-06-03

Peptides

Phospholipase D LiSicTox-alphaIA1bii: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phospholipase D LiSicTox-alphaIA1bii

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