SMTL ID : 8dnd.1

Crystal structure of Bothrops pirajai Piratoxin-I (PrTX-I) and synthetic inhibitor Varespladib (LY315920)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

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

VRD.1: 18 residues within 4Å: Chain A: L.2, L.5, G.6, I.9, P.17, A.18, Y.21, G.22, N.27, C.28, G.29, V.30, C.44, H.47, K.48, Y.51, K.60 Ligands: VRD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.9, A:P.17, A:A.18, A:Y.21, A:V.30 Hydrogen bonds: A:G.29, A:H.47, A:K.48 Salt bridges: A:K.48, A:K.60 VRD.2: 17 residues within 4Å: Chain A: L.2, F.3, G.6, K.7, L.10, N.16, P.17, A.18, K.19 Chain B: A.23, L.31, Y.109, H.110, L.111, K.112, P.113 Ligands: VRD.1 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.31, B:P.113, A:F.3, A:F.3, A:K.7, A:L.10, A:P.17 Hydrogen bonds: B:H.110, B:K.112, A:A.18, A:K.19 VRD.4: 18 residues within 4Å: Chain A: V.30, K.112 Chain B: L.2, L.5, G.6, I.9, P.17, A.18, Y.21, N.27, C.28, G.29, C.44, H.47, K.48, Y.51, K.60, L.96 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.5, B:I.9, B:P.17, B:A.18, B:Y.21, B:L.96, A:V.30 Hydrogen bonds: B:N.27, B:G.29, B:K.48 Salt bridges: B:K.48, B:K.60

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

SO4.3: 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, A:R.33 Salt bridges: A:R.33, A:K.52 SO4.5: 1 residues within 4Å: Chain B: K.35 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.35 SO4.6: 4 residues within 4Å: Chain B: K.19, K.105, R.108 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.108 Salt bridges: B:K.19, B:K.105, B:R.108 SO4.7: 5 residues within 4Å: Chain B: K.15, N.16, K.19, S.20 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.16 Salt bridges: B:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salvador, G.H.M. et al., Structural basis of the myotoxic inhibition of the Bothrops pirajai PrTX-I by the synthetic varespladib. Biochimie (2023)

Release Date

2023-08-02

Peptides

Basic phospholipase A2 homolog piratoxin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Basic phospholipase A2 homolog piratoxin-1

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