SMTL ID : 8r4y.1

Homotrimer for the lumenal domain of Vacuolar Sorting Receptor 1 (VSR1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: R.166, Q.207, T.209, Y.266, N.270 Ligands: MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 NAG-NAG-BMA-MAN.5: 6 residues within 4Å: Chain B: R.166, Q.207, T.209, Y.266, N.270 Ligands: MAN.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.166, B:R.166 NAG-NAG-BMA-MAN.9: 6 residues within 4Å: Chain C: R.166, Q.207, T.209, Y.266, N.270 Ligands: MAN.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.166, C:R.166

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.2: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) MAN.6: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) MAN.10: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP)

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: K.407, N.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.407, A:K.407 NAG.4: 2 residues within 4Å: Chain A: Q.123, N.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.123 NAG.7: 2 residues within 4Å: Chain B: K.407, N.410 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.407, B:K.407 NAG.8: 2 residues within 4Å: Chain B: Q.123, N.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.123 NAG.11: 2 residues within 4Å: Chain C: K.407, N.410 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.407, C:K.407 NAG.12: 2 residues within 4Å: Chain C: Q.123, N.124 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borges, R.J. et al., The crystal structure of Vacuolar Sorting Receptor 1 (VSR1) lumenal domain reveals a stable domain-swapped trimer and a potential new cargo binding site. To Be Published

Release Date

2025-08-13

Peptides

Vacuolar-sorting receptor 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Vacuolar-sorting receptor 1