MolNFT v1 · #128316 · protein

Monomeric mouse sortilin extracellular domain

5NMR: “Monomeric mouse sortilin extracellular domain”. X-ray diffraction, 2 ligands (NAG, CA), 3 pockets (best druggability 0.53). MolNFT v1 #128316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NMR
Type: protein
Length: 590 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sortilin
UniProt: Q6PHU5
Ligands: NAG, CA
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sortilin	protein	590	5% helix, 44% strand	Q6PHU5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.53	0.77	34	empty
2	129	0.46	0.77	23	empty
3	141	0.42	0.75	25	empty

Modifications

Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5NMR · Monomeric mouse Sortilin extracellular domain · 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 0.99

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 5NMR · PDBe 5NMR · UniProt Q6PHU5

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