SMTL ID : 2ph4.2 (1 other biounit)

Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: V.30, G.31, R.33, R.48 Chain B: F.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.31 Water bridges: A:R.48 Salt bridges: A:R.33, A:R.48 SO4.2: 2 residues within 4Å: Chain A: R.33, K.52 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.33, A:R.33 Salt bridges: A:R.33, A:K.52 SO4.4: 3 residues within 4Å: Chain B: V.30, R.33, R.48 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.48 Salt bridges: B:R.33, B:R.48 SO4.5: 4 residues within 4Å: Chain A: K.60 Chain B: Y.20, K.105, R.108 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Water bridges: B:T.19, B:T.19, B:Y.20, B:K.105 Salt bridges: B:K.105, B:R.108, A:K.60 SO4.6: 2 residues within 4Å: Chain B: R.33, K.52 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.52, B:K.52 Salt bridges: B:R.33, B:K.52 SO4.8: 5 residues within 4Å: Chain C: V.30, G.31, R.33, R.48 Chain D: F.109 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.31 Water bridges: C:R.48 Salt bridges: C:R.33, C:R.48 SO4.9: 2 residues within 4Å: Chain C: R.33, K.52 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.33, C:R.33 Salt bridges: C:R.33, C:K.52 SO4.11: 3 residues within 4Å: Chain D: V.30, R.33, R.48 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.48 Salt bridges: D:R.33, D:R.48 SO4.12: 4 residues within 4Å: Chain C: K.60 Chain D: Y.20, K.105, R.108 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Water bridges: D:T.19, D:T.19, D:Y.20, D:K.105 Salt bridges: D:K.105, D:R.108, C:K.60 SO4.13: 2 residues within 4Å: Chain D: R.33, K.52 4 PLIP interactions: 4 interactions with chain D Water bridges: D:K.52, D:K.52 Salt bridges: D:R.33, D:K.52

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: L.5, V.9, Y.21, G.29 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.29, A:H.47 PEG.7: 7 residues within 4Å: Chain B: L.5, P.17, V.18, Y.21, T.22, C.44, H.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.22, B:T.22, B:H.47 PEG.10: 4 residues within 4Å: Chain C: L.5, V.9, Y.21, G.29 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.29, C:H.47 PEG.14: 7 residues within 4Å: Chain D: L.5, P.17, V.18, Y.21, T.22, C.44, H.47 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.22, D:T.22, D:H.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M.T. et al., Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus. Toxicon (2008)

Release Date

2008-03-18

Peptides

Zhaoermiatoxin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Zhaoermiatoxin

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