SMTL ID : 3cyl.1

Crystal structure of Piratoxin I (a myotoxic Lys49-PLA2) complexed with alpha-tocopherol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: G.32, R.33, K.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.33 Water bridges: A:R.33 Salt bridges: A:R.33, A:K.52 SO4.2: 3 residues within 4Å: Chain A: K.19, K.105, R.108 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.15, A:K.19, A:K.105, A:R.108 SO4.3: 3 residues within 4Å: Chain A: T.72, I.94, R.97 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.72, A:K.90 Salt bridges: A:R.97 SO4.5: 4 residues within 4Å: Chain B: K.19, K.105, R.108 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.19, B:K.105, B:R.108 SO4.6: 5 residues within 4Å: Chain B: G.14, K.15, N.16, K.19 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.14, B:N.16 Water bridges: B:N.16 Salt bridges: B:K.19

2 x VIT: VITAMIN E(Non-covalent)

VIT.4: 13 residues within 4Å: Chain A: L.2, G.6, K.7, L.10, P.17, Y.21, G.22, C.28, G.29, V.30, K.48 Chain B: K.60 Ligands: VIT.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.7, A:L.10, A:P.17, A:P.17, A:V.30 Hydrogen bonds: B:K.60 VIT.7: 19 residues within 4Å: Chain A: V.30, L.31, K.60, L.111, K.112, P.113 Chain B: L.2, F.3, G.6, K.7, L.10, P.17, Y.21, G.22, G.29, H.47, K.48, Y.51 Ligands: VIT.4 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:V.30, A:L.111, A:K.112, A:P.113, B:L.2, B:L.2, B:L.2, B:F.3, B:L.10, B:P.17, B:K.48, B:Y.51 pi-Cation interactions: B:K.48

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.8: 7 residues within 4Å: Chain B: F.3, K.7, L.10, Q.11, Y.66, S.67, W.68 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.3, B:K.7 Hydrogen bonds: B:K.7 Water bridges: B:Y.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

dos Santos, J.I. et al., Comparative structural studies on Lys49-phospholipases A(2) from Bothrops genus reveal their myotoxic site. J.Struct.Biol. (2009)

Release Date

2009-05-05

Peptides

Phospholipase A2 homolog 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phospholipase A2 homolog 2

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