SMTL ID : 6pwh.1

Cystal structure of Myotoxin II from Bothrops moojeni co-crystallized with Varespladib (LY315920)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

VRD.1: 16 residues within 4Å: Chain A: L.2, L.5, G.6, I.9, A.18, Y.21, G.22, N.27, C.28, G.29, C.44, H.47, K.48, Y.51 Chain B: P.114, F.115 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.5, A:L.5, A:I.9, A:A.18, A:Y.21, B:P.114, B:F.115, B:F.115 Hydrogen bonds: A:G.29, A:G.29, A:C.44, A:H.47, A:K.48, A:K.48 Salt bridges: A:K.48 VRD.4: 16 residues within 4Å: Chain A: F.115 Chain B: L.2, L.5, G.6, I.9, P.17, A.18, Y.21, G.22, N.27, C.28, G.29, C.44, H.47, K.48, Y.51 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.2, B:I.9, B:P.17, B:A.18, B:Y.21, A:F.115, A:F.115 Hydrogen bonds: B:G.29, B:H.47, B:K.48 Salt bridges: B:K.48

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: K.106, Y.107, N.110, Y.111, L.112 No protein-ligand interaction detected (PLIP) DMS.3: 5 residues within 4Å: Chain A: K.53, T.55, G.56, C.81, E.84 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salvador, G.H.M. et al., Structural basis for phospholipase A2-like toxin inhibition by the synthetic compound Varespladib (LY315920). Sci Rep (2019)

Release Date

2019-12-04

Peptides

Basic phospholipase A2 homolog 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Basic phospholipase A2 homolog 2

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