SMTL ID : 6mry.2 (5 other biounits)

NoD173 plant defensin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 11 residues within 4Å: Chain A: S.36, K.37, V.38, L.39, R.41, L.43 Chain B: S.36, K.37, V.38, L.39, R.41 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.36, A:K.37, A:V.38, A:L.39, A:R.41, B:S.36, B:K.37, B:V.38, B:L.39, B:R.41 Salt bridges: A:K.5, A:R.41, B:R.41, B:R.41

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 1 residues within 4Å: Chain A: R.40 No protein-ligand interaction detected (PLIP) EDO.3: 1 residues within 4Å: Chain A: N.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 EDO.4: 2 residues within 4Å: Chain A: H.34, K.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.37, A:K.37

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: E.28, F.30 Ligand excluded by PLIP

1 x I3C: 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid(Non-covalent)

I3C.6: 4 residues within 4Å: Chain B: K.29, T.31, K.46, R.47 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.31 Hydrogen bonds: B:R.47 Water bridges: B:K.46, B:K.46 Salt bridges: B:K.46 Halogen bonds: B:K.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lay, F.T. et al., Structural and functional characterization of the membrane-permeabilizing activity ofNicotiana occidentalisdefensin NoD173 and protein engineering to enhance oncolysis. Faseb J. (2019)

Release Date

2019-04-24

Peptides

NoD173 defensin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

NoD173 defensin

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