SMTL ID : 4nt2.1

Crystal structure of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with lyso-sphingomyelin (d18:1) at 2.4 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x SPU: 2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium(Non-covalent)

SPU.1: 10 residues within 4Å: Chain A: F.57, M.60, D.61, H.143, H.144, G.145, I.148 Ligands: SPU.2, SO4.7, EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.60, A:I.148 Hydrogen bonds: A:D.61, A:G.145 SPU.2: 3 residues within 4Å: Chain A: I.148 Ligands: SPU.1, SO4.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.148

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

SO4.3: 3 residues within 4Å: Chain A: K.65, R.100, R.104 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.104, A:R.104 Salt bridges: A:K.65, A:R.100, A:R.104 SO4.4: 2 residues within 4Å: Chain A: R.149, K.150 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.149, A:K.150 SO4.5: 3 residues within 4Å: Chain A: K.19, S.182, N.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.185 Water bridges: A:S.15, A:S.182, A:S.186 SO4.6: 1 residues within 4Å: Chain A: R.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.12 SO4.7: 2 residues within 4Å: Ligands: SPU.1, SPU.2 No protein-ligand interaction detected (PLIP)

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

EDO.8: 8 residues within 4Å: Chain A: I.53, A.54, F.55, K.56, F.57, A.151, V.152 Ligands: SPU.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.56, A:F.57 EDO.9: 5 residues within 4Å: Chain A: V.80, M.83, D.84, L.197, K.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.84, A:L.197, A:K.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simanshu, D.K. et al., Arabidopsis Accelerated Cell Death 11, ACD11, Is a Ceramide-1-Phosphate Transfer Protein and Intermediary Regulator of Phytoceramide Levels. Cell Rep (2014)

Release Date

2014-02-05

Peptides

accelerated-cell-death 11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

accelerated-cell-death 11

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