SMTL ID : 9l4o.1

Arabidopsis thaliana protease-associated domain of vacuolar sorting receptor 1 in complexed with vicilin-like seed storage protein 22 C-terminal pentapeptide SDRFV (pH 5.8)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ACE- SER- ASP- ARG- PHE- VAL: Vicilin-like seed storage protein C-terminal pentapeptide(Non-covalent)

ACE-SER-ASP-ARG-PHE-VAL.1: 15 residues within 4Å: Chain A: G.1, S.2, R.3, V.5, V.6, R.78, C.81, Y.82, F.83, I.109, T.110, M.111, D.112, T.113, P.114 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.109, A:D.112 Hydrogen bonds: A:R.3, A:V.5, A:F.83, A:T.110, A:T.110, A:T.110, A:T.110, A:D.112 Water bridges: A:R.78, A:K.104 Salt bridges: A:R.78

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 4 residues within 4Å: Chain A: L.85, W.88, D.120, Y.123 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: Y.45, K.47 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.45

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

PEG.4: 4 residues within 4Å: Chain A: T.42, G.68, R.69, L.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68, A:L.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lui, S.N. et al., Structural insights into how vacuolar sorting receptor recognizes the C-terminal sorting determinant of a vicilin-like seed storage protein. Febs J. (2025)

Release Date

2025-09-10

Peptides

Vacuolar-sorting receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Vacuolar-sorting receptor 1

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