SMTL ID : 5nmt.1

Dimer structure of Sortilin ectodomain crystal form 1, 2.3A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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.1: 8 residues within 4Å: Chain A: A.322, A.323, N.324, E.325, F.329, N.373, T.375, Y.381 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.324 NAG-NAG.3: 7 residues within 4Å: Chain B: A.322, A.323, N.324, N.373, T.375, Y.381, P.449 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.449

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: H.68, Y.117, E.542, R.546, M.548, N.549, D.570, K.572 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.572 NAG-NAG-BMA.4: 8 residues within 4Å: Chain B: H.68, Y.117, E.542, R.546, S.547, M.548, N.549, D.570 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.572

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

NAG.5: 2 residues within 4Å: Chain A: N.129, N.130 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: E.650, N.651 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.650, A:N.651 NAG.9: 3 residues within 4Å: Chain B: N.126, N.129, N.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.129 NAG.10: 2 residues within 4Å: Chain B: E.650, N.651 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.650, B:E.650

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: I.511, N.512 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: Q.300 Ligand excluded by PLIP

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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