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Crystal structure of the synaptic protein neuroligin 4

Analyse Crystal structure of the synaptic protein neuroligin 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BE8
Type: protein
Length: 1,077 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuroligin-4, X-linked
UniProt: Q8N0W4
Ligands: NAG, NA, CL, PO4
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuroligin-4, X-linked	protein	543	38% helix, 16% strand	Q8N0W4
B	Neuroligin-4, X-linked	protein	534	36% helix, 16% strand	Q8N0W4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 6 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
FLC · Citrate anion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	440	0.75	0.84	65	empty
2	77	0.75	0.98	29	CL, PO4
3	60	0.71	0.97	30	PO4, CL
4	216	0.69	0.85	52	empty
5	340	0.62	0.78	45	empty

Interfaces

1 interface between chains.

A–B · 880 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3BE8 · Crystal structure of the synaptic protein neuroligin 4 · the same entry in another collection · chain A against A, TM-score 1.00
Q8N0W4 · AlphaFold monomer V2.0 prediction for neuroligin-4, X-linked (Q8N0W4) · a predicted model of the same protein · chain B 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 Q8N0W4
Elsewhere: RCSB PDB 3BE8 · PDBe 3BE8 · UniProt Q8N0W4

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