MolNFT v1 · #175046 · protein

Crystal structure of mouse neuroligin-3

7CEE: “Crystal structure of mouse neuroligin-3”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.63). MolNFT v1 #175046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7CEE
Type: protein
Length: 1,067 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuroligin-3
UniProt: Q8BYM5
Ligands: NAG
Pockets: 11 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuroligin-3	protein	534	37% helix, 15% strand	Q8BYM5
B	Neuroligin-3	protein	533	38% helix, 15% strand	Q8BYM5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B

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

Pockets

11 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	196	0.63	0.83	45	empty
2	361	0.62	0.78	58	empty
3	306	0.57	0.76	27	empty
4	132	0.54	0.81	33	empty
5	265	0.53	0.75	22	empty

Interfaces

1 interface between chains.

A–B · 846 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

7CEE · Crystal structure of mouse neuroligin-3 · the same entry in another collection · chain A against A, TM-score 1.00
Q8BYM5 · AlphaFold monomer V2.0 prediction for neuroligin-3 (Q8BYM5) · 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 Q8BYM5
Elsewhere: RCSB PDB 7CEE · PDBe 7CEE · UniProt Q8BYM5

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