SMTL ID : 4msl.1

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 6 residues within 4Å: Chain A: A.278, A.279, N.280, N.329, T.331, Y.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.281

1 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: 9 residues within 4Å: Chain A: E.71, D.72, Y.73, K.75, S.503, M.504, N.505, D.526, R.578 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: V.35, L.37, T.493, G.494, L.495, W.509, W.520 No protein-ligand interaction detected (PLIP)

1 x 2ET: N-[(7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methyl]-L-leucine(Non-covalent)

2ET.4: 11 residues within 4Å: Chain A: Y.227, S.228, F.229, F.237, S.239, R.248, F.273, Y.274, S.275, Y.318, G.323 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.237, A:F.273, A:Y.318 Hydrogen bonds: A:S.239, A:S.239, A:Y.274, A:Y.274 Salt bridges: A:R.248 pi-Stacking: A:F.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andersen, J.L. et al., Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-02-12

Peptides

Sortilin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sortilin

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