SMTL ID : 3wsx.1

SorLA Vps10p domain in ligand-free form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: F.126, N.130, S.132, A.156, Y.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.132, A:S.132 NAG.2: 6 residues within 4Å: Chain A: Y.65, Y.113, V.568, N.588, T.590, D.591 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.113, A:V.568 Hydrogen bonds: A:N.588, A:D.591 NAG.3: 3 residues within 4Å: Chain A: V.644, N.646, T.707 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: K.221, H.241, E.242, G.245, R.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.242 Water bridges: A:K.221 Salt bridges: A:K.221, A:H.241, A:R.270 PO4.5: 4 residues within 4Å: Chain A: R.275, D.325, R.388 Ligands: EDO.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.325, A:D.325, A:S.327 Water bridges: A:A.326 Salt bridges: A:R.275, A:R.388 PO4.6: 5 residues within 4Å: Chain A: V.78, H.80, R.94, Q.138, F.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.138 Salt bridges: A:H.80, A:R.94 PO4.7: 3 residues within 4Å: Chain A: D.145, R.148, S.188 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.145, A:D.145, A:S.188, A:S.188 Water bridges: A:R.148, A:R.148, A:S.188 Salt bridges: A:K.147, A:R.148

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 9 residues within 4Å: Chain A: E.320, Y.321, Y.322, C.334, V.335, S.336, H.337, T.342, Y.363 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.320, A:C.334, A:S.336, A:H.337 EDO.9: 4 residues within 4Å: Chain A: S.496, K.603, R.625, P.628 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.496, A:R.625 Water bridges: A:R.501 EDO.10: 5 residues within 4Å: Chain A: E.320, G.368, D.372, V.375, R.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.320, A:R.376 EDO.11: 4 residues within 4Å: Chain A: E.348, K.353, D.657, R.701 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.353, A:D.657, A:R.701 EDO.12: 6 residues within 4Å: Chain A: A.324, Y.377, F.386, H.387, R.388 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.377, A:R.388 EDO.13: 4 residues within 4Å: Chain A: V.670, C.671, R.698, Y.700 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.700, A:Y.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitago, Y. et al., Structural basis for amyloidogenic peptide recognition by sorLA. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-02-04

Peptides

Sortilin-related receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sortilin-related receptor