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Dimer structure of sortilin ectodomain crystal form 3, 4.0 ångström

Analyse Dimer structure of sortilin ectodomain crystal form 3, 4.0 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NNJ
Type: protein
Length: 2,590 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sortilin
UniProt: Q6PHU5
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Sortilin	protein	648	5% helix, 41% strand	Q6PHU5
C	Sortilin	protein	646	5% helix, 42% strand	Q6PHU5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, D, C
BMA · beta-D-mannopyranose · sugar · 8 copies

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.71	0.94	27	empty
2	109	0.70	0.92	29	empty
3	99	0.70	0.92	28	empty
4	86	0.69	0.93	28	empty
5	597	0.68	0.77	57	empty

Interfaces

3 interfaces between chains.

A–B · 2086 Å² buried · 6 hydrogen bonds · protein-protein
D–C · 1927 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 278 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 31 disulfide, 13 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

5NNJ · Dimer structure of Sortilin ectodomain crystal form 3, 4.0 Angstrom · 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 C 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 5NNJ · PDBe 5NNJ · UniProt Q6PHU5

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