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Crystal structure of the extracellular esterase domain of neuroligin-1

Analyse Crystal structure of the extracellular esterase domain of neuroligin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BIX
Type: protein
Length: 2,220 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuroligin-1
UniProt: Q62765
Ligands: NAG, NI
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Neuroligin-1	protein	555	35% helix, 15% strand	Q62765

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
NI · Nickel (II) ion · metal · 2 copies · chains A, D, B, C
EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.88	0.91	102	empty
2	1175	0.87	0.88	117	empty
3	432	0.79	0.87	52	empty
4	350	0.76	0.87	52	empty
5	76	0.66	0.92	24	empty

Interfaces

5 interfaces between chains.

B–D · 1148 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 729 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 678 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 329 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 315 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

3BIX · Crystal structure of the extracellular esterase domain of Neuroligin-1 · the same entry in another collection · chain A against A, TM-score 1.00
Q62765 · AlphaFold monomer V2.0 prediction for neuroligin-1 (Q62765) · 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 Q62765
Elsewhere: RCSB PDB 3BIX · PDBe 3BIX · UniProt Q62765

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