SMTL ID : 7lye.1

Myotoxin I from Bothrops moojeni co-crystallized with synthetic inhibitor Varespladib (LY315920)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x VRD: ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid(Non-covalent)

VRD.1: 17 residues within 4Å: Chain A: L.2, L.5, G.6, I.9, P.17, V.18, Y.21, N.27, C.28, G.29, V.30, C.44, H.47, K.48, Y.51, K.60, V.92 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.5, A:I.9, A:P.17, A:V.18, A:Y.21 Hydrogen bonds: A:N.27, A:G.29, A:K.48, A:K.48 Salt bridges: A:K.48, A:K.60 VRD.2: 16 residues within 4Å: Chain B: L.2, L.5, G.6, I.9, P.17, V.18, Y.21, N.27, C.28, G.29, C.44, H.47, K.48, Y.51, K.60, V.92 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.5, B:I.9, B:P.17, B:V.18, B:Y.21 Hydrogen bonds: B:N.27, B:G.29, B:K.48, B:K.48 Salt bridges: B:K.48, B:K.60 VRD.4: 15 residues within 4Å: Chain C: L.2, L.5, G.6, I.9, P.17, V.18, Y.21, N.27, C.28, G.29, V.30, C.44, H.47, K.48, Y.51 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.2, C:L.2, C:I.9, C:P.17, C:P.17, C:V.18, C:Y.21 Hydrogen bonds: C:N.27, C:G.29, C:K.48 Salt bridges: C:K.48 VRD.5: 15 residues within 4Å: Chain D: L.2, L.5, G.6, I.9, P.17, V.18, Y.21, N.27, C.28, G.29, C.44, H.47, K.48, Y.51, K.60 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.2, D:L.2, D:L.5, D:I.9, D:P.17, D:P.17, D:V.18, D:Y.21 Hydrogen bonds: D:N.27, D:G.29, D:H.47, D:K.48 Salt bridges: D:K.48, D:K.60

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

PE4.3: 12 residues within 4Å: Chain A: K.7, L.10, Q.11, G.14, Y.66, W.68 Chain B: K.7, L.10, Q.11, G.14, Y.66, W.68 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.7, A:Q.11, B:K.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salvador, G.H.M. et al., The synthetic varespladib molecule is a multi-functional inhibitor for PLA 2 and PLA 2 -like ophidic toxins. Biochim Biophys Acta Gen Subj (2021)

Release Date

2021-05-19

Peptides

Basic phospholipase A2 homolog BomoTx: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Basic phospholipase A2 homolog BomoTx