SMTL ID : 5znn.1

Crystal structure of ligand-free form of the Vps10 ectodomain of Sortilin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 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: 8 residues within 4Å: Chain A: Y.73, E.498, R.502, S.503, M.504, N.505, D.526 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.73 NAG-NAG-BMA.3: 7 residues within 4Å: Chain B: A.278, A.279, N.280, N.329, T.331, R.334, Y.337 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.334 NAG-NAG-BMA.4: 7 residues within 4Å: Chain B: Y.73, E.498, R.502, M.504, N.505, D.526, K.528 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.528 NAG-NAG-BMA.5: 3 residues within 4Å: Chain B: E.344, E.606, N.607 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain A: A.278, A.279, N.280, E.281, N.329, T.331, R.334, Y.337 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.334

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

NAG.6: 2 residues within 4Å: Chain A: N.85, N.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:N.86 NAG.7: 3 residues within 4Å: Chain A: H.362, E.606, N.607 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.607 NAG.14: 2 residues within 4Å: Chain B: N.85, N.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.85

5 x NA: SODIUM ION(Non-functional Binders)

NA.8: 5 residues within 4Å: Chain A: E.110, V.111, S.115, G.117, H.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.111, A:V.111, A:S.115 NA.9: 5 residues within 4Å: Chain A: G.185, P.186, N.187, N.188, I.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.187, A:N.187, A:I.189 NA.10: 3 residues within 4Å: Chain A: S.43, E.498 Ligands: NAG-NAG-BMA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.43, A:S.43 NA.15: 2 residues within 4Å: Chain B: N.149, S.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.150 NA.16: 4 residues within 4Å: Chain B: T.141, Q.142, A.155, L.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.142, B:L.156

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.12: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.251 ACT.13: 5 residues within 4Å: Chain A: I.348, H.384, L.395, V.423 Chain B: P.56 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.423 Salt bridges: A:H.384, A:H.386 ACT.17: 5 residues within 4Å: Chain A: P.56 Chain B: I.348, H.384, Y.389, L.395 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.348 Salt bridges: B:H.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yabe-Wada, T. et al., Crystal structure of the ligand-free form of the Vps10 ectodomain of dimerized Sortilin at acidic pH. FEBS Lett. (2018)

Release Date

2018-07-18

Peptides

Sortilin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sortilin