SMTL ID : 5vfm.1

Crystal structure of BnSP-7 from Bothrops pauloensis complexed with p-coumaric acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x ME2: 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE(Non-covalent)

ME2.1: 8 residues within 4Å: Chain A: L.2, L.5, G.6, P.17, A.18, Y.21, G.29 Chain B: L.111 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.2, A:L.5 ME2.6: 5 residues within 4Å: Chain A: L.111 Chain B: L.2, L.5, G.6, A.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.2, B:L.5, A:L.111

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

SO4.2: 4 residues within 4Å: Chain A: K.15, N.16, K.19 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16 Salt bridges: A:K.15, A:K.19 SO4.3: 5 residues within 4Å: Chain A: K.15, K.19, K.105, R.108 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.15, A:K.19, A:K.105, A:R.108 SO4.4: 3 residues within 4Å: Chain A: G.32, R.33, K.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33 Salt bridges: A:R.33, A:K.52 SO4.5: 5 residues within 4Å: Chain A: E.4, K.7, R.63, Y.64, Y.66 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.7, A:K.7, A:Y.64 Salt bridges: A:K.7, A:R.63 SO4.7: 5 residues within 4Å: Chain B: G.14, K.15, N.16, K.19 Ligands: HC4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.16 Salt bridges: B:K.15, B:K.19 SO4.8: 2 residues within 4Å: Chain B: G.32, R.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.33 Salt bridges: B:R.33, B:K.52 SO4.9: 2 residues within 4Å: Chain B: P.36, R.42 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.42, B:R.42 Salt bridges: B:R.42 SO4.10: 2 residues within 4Å: Chain B: I.94, R.97 8 PLIP interactions: 8 interactions with chain B Water bridges: B:E.12, B:K.90, B:K.90, B:K.90, B:R.97, B:R.97, B:R.97 Salt bridges: B:R.97 SO4.11: 3 residues within 4Å: Chain B: C.49, C.50, K.53 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.53

1 x HC4: 4'-HYDROXYCINNAMIC ACID(Non-covalent)

HC4.12: 7 residues within 4Å: Chain A: K.19 Chain B: K.15, K.19, K.105, R.108, Y.109 Ligands: SO4.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.108, B:Y.109 Salt bridges: B:K.19, A:K.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Lima, L.F.G. et al., Structural studies with BnSP-7 reveal an atypical oligomeric conformation compared to phospholipases A2-like toxins. Biochimie (2017)

Release Date

2017-12-20

Peptides

Basic phospholipase A2 homolog BnSP-7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Basic phospholipase A2 homolog BnSP-7

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