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Crystal structure of ligand-free form of the VPS10 ectodomain of sortilin

Analyse Crystal structure of ligand-free form of the VPS10 ectodomain of sortilin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZNN
Type: protein
Length: 1,293 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q6PHU5
Ligands: NAG, BMA, NA

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	644	—	Q6PHU5
B	—	protein	649	—	Q6PHU5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 4 copies
NA · Sodium ion · metal · 5 copies · chains A, B
ACT · Acetate ion · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

5ZNN · Crystal structure of ligand-free form of the Vps10 ectodomain of Sortilin · the same entry in another collection · chain A against A, TM-score 1.00
Q6PHU5 · AlphaFold monomer V2.0 prediction for sortilin (Q6PHU5) · a predicted model of the same protein · chain A against A, TM-score 0.90

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6PHU5
Elsewhere: RCSB PDB 5ZNN · PDBe 5ZNN · UniProt Q6PHU5

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