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Netrin-1 filament assembly

Analyse Netrin-1 filament assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LER
Type: protein
Length: 3,249 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Netrin-1
UniProt: Q90922
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Netrin-1	protein	410	6% helix, 30% strand	Q90922
B, G	Netrin-1	protein	403	7% helix, 25% strand	Q90922
C, E, F	Netrin-1	protein	409	5% helix, 23% strand	Q90922
D	Netrin-1	protein	402	5% helix, 28% strand	Q90922
H	Netrin-1	protein	404	7% helix, 26% strand	Q90922

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, B, C, E, D, F, G, H
MAN · alpha-D-mannopyranose · sugar · 16 copies
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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.85	0.88	76	empty
2	982	0.85	0.86	79	empty
3	991	0.85	0.86	99	empty
4	684	0.84	0.88	85	empty
5	909	0.84	0.86	95	empty

Interfaces

8 interfaces between chains.

C–E · 513 Å² buried · 8 hydrogen bonds · protein-protein
B–G · 409 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 288 Å² buried · 2 hydrogen bonds · protein-protein
D–H · 246 Å² buried · 2 hydrogen bonds · protein-protein
D–G · 200 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 139 disulfide, 32 glycan (disulfide, N-glycosylation).

Compared structures

7LER · Netrin-1 filament assembly · the same entry in another collection · chain H against H, TM-score 1.00
Q90922 · AlphaFold monomer V2.0 prediction for netrin-1 (Q90922) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q90922
Elsewhere: RCSB PDB 7LER · PDBe 7LER · UniProt Q90922

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