Research workbench
Crystal structure of the neuroligin-1/NEUREXIN-1BETA synaptic adhesion complex
Analyse Crystal structure of the neuroligin-1/NEUREXIN-1BETA synaptic adhesion complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BIW
- Type
- protein
- Length
- 2,840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin-1; Neurexin-1-beta
- UniProt
- Q62765, Q63373
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuroligin-1 | protein | 533 | 35% helix, 16% strand | Q62765 |
| E, F, G, H | Neurexin-1-beta | protein | 177 | 5% helix, 53% strand | Q63373 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains E, F, B, G, A, C, D
- CA · Calcium ion · metal · 6 copies · chains A, E, B, F, G, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.80 | 0.81 | 98 | empty |
| 2 | 291 | 0.71 | 0.84 | 43 | empty |
| 3 | 287 | 0.70 | 0.84 | 45 | empty |
| 4 | 85 | 0.70 | 0.94 | 17 | empty |
| 5 | 92 | 0.69 | 0.93 | 18 | empty |
Interfaces
11 interfaces between chains.
- B–C · 898 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 864 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 651 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 645 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 635 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 3BIW · Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex · the same entry in another collection · chain B against B, 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 1.00
- Q63373 · AlphaFold monomer V2.0 prediction for neurexin-1-beta (Q63373) · a predicted model of the same protein · chain E 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
- Every structure of UniProt Q63373
- Elsewhere: RCSB PDB 3BIW · PDBe 3BIW · UniProt Q62765 · UniProt Q63373
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