SMTL ID : 1y4l.1

Crystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.1: 15 residues within 4Å: Chain A: L.2, L.5, G.6, K.7, I.9, L.10, P.17, Y.21, N.27, C.28, G.29, C.44, H.47, K.48 Ligands: SVR.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.29, A:C.44, A:K.48 P33.5: 16 residues within 4Å: Chain A: L.111 Chain B: L.2, G.6, K.7, I.9, L.10, P.17, Y.21, G.22, N.27, C.28, G.29, C.44, H.47, K.48 Ligands: SVR.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.6, B:G.29, B:H.47, B:K.48

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 4 residues within 4Å: Chain A: K.19, K.105, R.108 Ligands: IPA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.105 IPA.3: 4 residues within 4Å: Chain A: K.15, N.16, K.19 Ligands: IPA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.16, A:K.19 IPA.6: 5 residues within 4Å: Chain B: L.54, T.55, S.80, C.81, E.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.53, B:T.55, B:E.84 IPA.7: 6 residues within 4Å: Chain B: G.14, K.15, N.16, K.19, S.20 Ligands: IPA.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.16 Hydrogen bonds: B:N.16 IPA.8: 4 residues within 4Å: Chain B: K.19, K.105, R.108 Ligands: IPA.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.105, B:R.108, B:R.108

1 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID(Non-covalent)

SVR.4: 27 residues within 4Å: Chain A: L.2, G.22, G.29, V.30, L.31, G.32, R.33, K.48, Y.51, K.52, P.59, K.60, K.61 Chain B: L.2, L.5, G.29, V.30, G.32, R.33, H.47, K.48, Y.51, K.52, K.60, K.61 Ligands: P33.1, P33.5 31 PLIP interactions: 15 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:L.2, A:L.2, A:V.30, A:R.33, A:K.48, A:P.59, A:K.60, B:L.2, B:L.5, B:V.30, B:R.33, B:K.48, B:K.48, B:Y.51, B:Y.51, B:K.52 Hydrogen bonds: A:L.31, A:R.33, B:K.60 Water bridges: A:G.22, B:G.22 Salt bridges: A:R.33, A:K.52, A:K.60, A:K.61, B:R.33, B:K.52, B:K.60, B:K.61, B:K.61 pi-Stacking: A:Y.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M.T. et al., Inhibition of Myotoxic Activity of Bothrops asper Myotoxin II by the Anti-trypanosomal Drug Suramin. J.Mol.Biol. (2005)

Release Date

2005-06-28

Peptides

Phospholipase A2 homolog 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phospholipase A2 homolog 2

Related Entries With Identical Sequence