SMTL ID : 5nnj.2 (1 other biounit)

Dimer structure of Sortilin ectodomain crystal form 3, 4.0 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

homo-dimer

Ligands

4 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: 6 residues within 4Å: Chain A: A.323, A.324, N.325, N.374, T.376, Y.382 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: H.69, S.88, Y.118, E.543, N.550, T.569, D.571, K.573 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.573 NAG-NAG-BMA.3: 7 residues within 4Å: Chain B: A.323, A.324, N.325, E.326, N.374, T.376, Y.382 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.325, B:E.326 NAG-NAG-BMA.4: 8 residues within 4Å: Chain B: S.88, Y.118, E.543, R.547, S.548, M.549, N.550, D.571 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: E.651, N.652 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.651, A:N.652 NAG.6: 2 residues within 4Å: Chain B: E.651, N.652 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.651, B:E.651, B:N.652

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
D

B
C

Sortilin

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