MolNFT v1 · #82359 · protein
Crystal structure of neurexin 1BETA/NEUROLIGIN 1 complex
3VKF · Neuroligin-1: “Crystal structure of neurexin 1BETA/NEUROLIGIN 1 complex”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 16 pockets (best druggability 0.69). MolNFT v1 #82359 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3VKF
- Type
- protein
- Length
- 1,441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin-1; Neurexin-1-beta
- UniProt
- Q62765, Q28142
- Ligands
- NAG, BMA, CA
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuroligin-1 | protein | 560 | 37% helix, 15% strand | Q62765 |
| B | Neuroligin-1 | protein | 527 | 35% helix, 16% strand | Q62765 |
| C, D | Neurexin-1-beta | protein | 177 | 5% helix, 53% strand | Q28142 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.69 | 0.97 | 18 | empty |
| 2 | 52 | 0.68 | 0.97 | 21 | empty |
| 3 | 268 | 0.67 | 0.83 | 44 | empty |
| 4 | 179 | 0.64 | 0.84 | 34 | empty |
| 5 | 322 | 0.59 | 0.77 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1103 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 649 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3VKF · Crystal Structure of Neurexin 1beta/Neuroligin 1 complex · 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 B against A, TM-score 0.99
- Q28142 · AlphaFold monomer V2.0 prediction for neurexin-1-beta (Q28142) · a predicted model of the same protein · chain C 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 Q28142
- Elsewhere: RCSB PDB 3VKF · PDBe 3VKF · UniProt Q62765 · UniProt Q28142
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