SMTL ID : 5nni.1

Dimer structure of Sortilin ectodomain crystal form 2, 3.2 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-dimer

Ligands

3 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.1: 8 residues within 4Å: Chain A: A.324, N.325, E.326, F.330, N.374, T.376, Y.382, P.450 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.326 NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: Y.118, E.543, R.547, M.549, N.550, D.571, K.573 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.573 NAG-NAG-BMA.4: 7 residues within 4Å: Chain B: S.88, Y.118, E.543, R.547, M.549, N.550, D.571 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.118 Hydrogen bonds: B:Y.118

1 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: 7 residues within 4Å: Chain B: A.324, N.325, E.326, N.374, T.376, Y.382, P.450 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.325, B:E.326 Hydrogen bonds: B:E.326

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

NAG.5: 2 residues within 4Å: Chain A: N.130, N.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.131 NAG.6: 3 residues within 4Å: Chain B: N.127, N.130, N.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leloup, N. et al., Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release. Nat Commun (2017)

Release Date

2017-11-29

Peptides

Sortilin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sortilin

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