SMTL ID : 6mry.4 (5 other biounits)

NoD173 plant defensin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 1 residues within 4Å: Chain A: R.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.40 PGE.4: 3 residues within 4Å: Chain B: Q.23, I.26, R.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.26, B:R.27

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

PEG.2: 8 residues within 4Å: Chain A: K.5, K.37, R.41, L.43 Chain B: K.5, R.41, L.43 Ligands: FLC.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.41, B:R.41, B:R.41 Water bridges: A:K.37

1 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 12 residues within 4Å: Chain A: S.36, K.37, V.38, L.39, R.41 Chain B: S.36, K.37, V.38, L.39, R.41, L.43 Ligands: PEG.2 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.39 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:R.41, A:R.41, B:K.37, B:R.41 Water bridges: B:H.34

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

EDO.5: 7 residues within 4Å: Chain B: F.11, I.14, C.15, I.16, A.17, P.20, C.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.16, B:A.17

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

CL.6: 2 residues within 4Å: Chain B: F.30, K.46 Ligand excluded by PLIP

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
D

B
L

NoD173 defensin

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