SMTL ID : 4cqk.6 (6 other biounits)

Crystal structure of ligand-bound NaD1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 10 residues within 4Å: Chain A: K.4, H.33, S.35, K.36, I.37, L.38, R.40, L.42 Chain B: R.40 Ligands: PIO.3 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.35, A:K.36, A:I.37, A:L.38, A:R.40 Water bridges: A:K.36, A:K.36, A:K.36, A:K.36, B:R.40, B:R.40 Salt bridges: A:K.4, A:K.4, A:H.33, A:K.36, A:R.40, B:R.40 PIO.3: 10 residues within 4Å: Chain A: R.40 Chain B: K.4, H.33, S.35, K.36, I.37, L.38, R.40, L.42 Ligands: PIO.1 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.36, B:I.37, B:L.38, B:R.40 Water bridges: B:K.4, B:K.4, B:R.40 Salt bridges: B:K.4, B:K.4, B:H.33, B:K.36, B:R.40, A:R.40

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

SO4.2: 3 residues within 4Å: Chain A: R.1, C.47 Chain B: N.8 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.8, A:C.47 Water bridges: A:R.1, A:R.1 Salt bridges: A:R.1 SO4.4: 2 residues within 4Å: Chain B: R.1, C.47 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:E.27, B:R.1, B:C.47, B:C.47 Hydrogen bonds: B:C.47 Salt bridges: B:R.1 SO4.5: 1 residues within 4Å: Chain B: R.21 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poon, I.K.H. et al., Phosphoinositide-Mediated Oligomerization of a Defensin Induces Cell Lysis. Elife (2014)

Release Date

2014-04-16

Peptides

FLOWER-SPECIFIC DEFENSIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
G

FLOWER-SPECIFIC DEFENSIN

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