SMTL ID : 6eho.1

Dimer of the Sortilin Vps10p domain at low pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 9 residues within 4Å: Chain A: A.322, A.323, N.324, D.325, F.329, N.373, T.375, R.378, Y.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.325 NAG-NAG-BMA-MAN-MAN.4: 9 residues within 4Å: Chain B: A.322, A.323, N.324, D.325, F.329, N.373, T.375, R.378, Y.381 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.325, B:D.325

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

NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: Y.117, K.119, E.542, R.546, S.547, M.548, N.549, D.570 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 8 residues within 4Å: Chain B: Y.117, K.119, E.542, R.546, S.547, M.548, N.549, D.570 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain A: N.129, N.130, R.163 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.129, N.130, R.163 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Januliene, D. et al., Acidic Environment Induces Dimerization and Ligand Binding Site Collapse in the Vps10p Domain of Sortilin. Structure (2017)

Release Date

2017-12-06

Peptides

Sortilin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Sortilin