SMTL ID : 4rw3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 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: IPD.4 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

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

PEG.2: 3 residues within 4Å: Chain A: G.223, L.224, S.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.223, A:L.224, A:S.225 PEG.3: 2 residues within 4Å: Chain A: Y.67, Y.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.67 Water bridges: A:S.58, A:E.66

1 x IPD: D-MYO-INOSITOL-1-PHOSPHATE(Non-covalent)

IPD.4: 12 residues within 4Å: Chain A: H.34, E.54, D.56, H.70, D.114, K.116, S.189, S.213, Y.245, W.247, M.267 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.116, A:S.189, A:S.213, A:Y.245 Water bridges: A:M.35, A:D.114, A:K.116, A:S.155, A:S.189, A:S.189, A:Y.245

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: G.190, N.191, D.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192

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

OCA.6: 3 residues within 4Å: Chain A: A.281, K.285 Ligands: PLM.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.281 Salt bridges: A:K.285

1 x SHV: HEPTANOIC ACID(Non-covalent)

SHV.7: 5 residues within 4Å: Chain A: G.198, Y.201, I.206, T.207, F.240 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.201 Hydrogen bonds: A:G.198 Water bridges: A:K.199, A:F.240

2 x DKA: DECANOIC ACID(Non-covalent)

DKA.8: 4 residues within 4Å: Chain A: P.73, C.74, T.217, C.219 No protein-ligand interaction detected (PLIP) DKA.12: 4 residues within 4Å: Chain A: I.165, K.169, M.181, I.206 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.165, A:K.169, A:I.206 Salt bridges: A:K.169

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.9: 5 residues within 4Å: Chain A: N.218, D.250, K.251, Y.270, V.273 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.250, A:Y.270 PLM.10: 3 residues within 4Å: Chain A: N.279, K.284 Ligands: OCA.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.279 Salt bridges: A:K.284 PLM.11: 7 residues within 4Å: Chain A: N.62, N.64, D.127, K.130, K.131, K.134, Q.171 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.62, A:K.130, A:K.134 Salt bridges: A:K.131, A:K.134

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

TDA.13: 3 residues within 4Å: Chain A: N.160, Y.162, K.203 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.162, A:K.203 Salt bridges: A:K.203

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