SMTL ID : 4yv5.1

Crystal Structure of Myotoxin II from Bothrops moojeni complexed to Suramin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: 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 SO4.2: 5 residues within 4Å: Chain A: K.15, N.16, K.19 Ligands: SO4.1, SVR.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16 Salt bridges: A:K.15, A:K.19 SO4.5: 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 SO4.6: 2 residues within 4Å: Chain A: K.106, Y.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.107 Salt bridges: A:K.106 SO4.8: 4 residues within 4Å: Chain B: K.15, K.19, K.105, R.108 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.15, B:K.19, B:K.105, B:R.108 SO4.9: 4 residues within 4Å: Chain B: K.15, N.16, K.19 Ligands: SVR.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.16 Salt bridges: B:K.15, B:K.19 SO4.11: 3 residues within 4Å: Chain B: G.32, R.33, K.52 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.33 Salt bridges: B:R.33, B:K.52

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

PE4.3: 8 residues within 4Å: Chain A: K.7, L.10, Q.11, G.14, Y.66, S.67, W.68 Ligands: SVR.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.7, A:Q.11, A:Y.66 Water bridges: A:W.68

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 14 residues within 4Å: Chain A: L.2, G.6, I.9, A.18, Y.21, N.27, C.28, G.29, C.44, H.47 Chain B: V.30, Y.111, K.113, P.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.29 1PE.10: 14 residues within 4Å: Chain A: V.30, Y.111, P.114 Chain B: L.2, I.9, P.17, A.18, Y.21, N.27, C.28, G.29, C.44, H.47, K.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.29, B:C.44

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

SVR.7: 15 residues within 4Å: Chain A: N.104, K.105, K.106, Y.109, Y.111, L.112, F.115 Chain B: F.3, G.6, K.7, L.10, N.16, P.17, R.63 Ligands: SO4.9 23 PLIP interactions: 7 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:K.7, B:L.10, B:N.16, A:K.105, A:K.106, A:Y.111, A:Y.111, A:Y.111, A:L.112, A:F.115 Hydrogen bonds: B:R.63, A:N.104 Water bridges: B:K.7, A:K.105, A:K.105, A:Y.109 Salt bridges: B:K.7, A:K.106, A:K.106 pi-Cation interactions: B:K.7 pi-Stacking: A:Y.109, A:F.115, A:F.115 SVR.12: 16 residues within 4Å: Chain A: F.3, G.6, K.7, L.10, N.16, P.17, R.63 Chain B: N.104, K.105, K.106, Y.109, Y.111, L.112, F.115 Ligands: SO4.2, PE4.3 20 PLIP interactions: 7 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:K.7, A:L.10, A:N.16, A:P.17, B:K.106, B:K.106, B:Y.111, B:Y.111, B:Y.111, B:L.112, B:F.115 Hydrogen bonds: A:R.63, B:N.104, B:N.104 Salt bridges: A:K.7, B:K.106 pi-Cation interactions: A:K.7 Water bridges: B:K.105 pi-Stacking: B:F.115, B:F.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salvador, G.H. et al., Structural and functional evidence for membrane docking and disruption sites on phospholipase A2-like proteins revealed by complexation with the inhibitor suramin. Acta Crystallogr. D Biol. Crystallogr. (2015)

Release Date

2015-10-14

Peptides

Basic phospholipase A2 homolog 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Basic phospholipase A2 homolog 2

Related Entries With Identical Sequence