Research workbench
Crystal structure of a synaptic adhesion complex
Analyse Crystal structure of a 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
- 3B3Q
- Type
- protein
- Length
- 1,446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NLGN1 protein; NRXN1 protein
- UniProt
- Q4KMN5, A4FVB9
- Ligands
- NAG, CA
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NLGN1 protein | protein | 536 | 36% helix, 15% strand | Q4KMN5 |
| E, F | NRXN1 protein | protein | 187 | 3% helix, 49% strand | A4FVB9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.84 | 48 | empty |
| 2 | 337 | 0.72 | 0.84 | 49 | empty |
| 3 | 78 | 0.67 | 0.93 | 20 | empty |
| 4 | 80 | 0.66 | 0.92 | 19 | empty |
| 5 | 359 | 0.62 | 0.78 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 874 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 663 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 627 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3B3Q · Crystal structure of a synaptic adhesion complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4KMN5
- Every structure of UniProt A4FVB9
- Elsewhere: RCSB PDB 3B3Q · PDBe 3B3Q · UniProt Q4KMN5 · UniProt A4FVB9
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