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Netrin 4 lacking the C-terminal domain

Analyse Netrin 4 lacking the C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WNX
Type: protein
Length: 429 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Netrin-4
UniProt: Q9JI33
Ligands: TAM, NAG, CA
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Netrin-4	protein	429	7% helix, 28% strand	Q9JI33

Ligands and binding sites

TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
CA · Calcium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.28	0.75	12	empty

Modifications

Observed in the structure: 20 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4WNX · Netrin 4 lacking the C-terminal Domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9JI33 · AlphaFold monomer V2.0 prediction for netrin-4 (Q9JI33) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9JI33
Elsewhere: RCSB PDB 4WNX · PDBe 4WNX · UniProt Q9JI33

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