MolNFT v1 · #111025 · protein
Structural characterization of a synaptic adhesion complex
4YEB · Latrophilin-3: “Structural characterization of a synaptic adhesion complex”. X-ray diffraction, 2 ligands (NAG, CA), 5 pockets (best druggability 0.73). MolNFT v1 #111025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YEB
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Latrophilin-3; Fibronectin leucine rich transmembrane protein 3
- UniProt
- Q80TS3, Q8BGT1
- Ligands
- NAG, CA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Latrophilin-3 | protein | 267 | 2% helix, 49% strand | Q80TS3 |
| B | Fibronectin leucine rich transmembrane protein 3 | protein | 321 | 6% helix, 16% strand | Q8BGT1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.73 | 0.77 | 73 | empty |
| 2 | 160 | 0.53 | 0.79 | 22 | empty |
| 3 | 90 | 0.43 | 0.79 | 17 | empty |
| 4 | 139 | 0.38 | 0.73 | 27 | empty |
| 5 | 54 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4YEB · Structural characterization of a synaptic adhesion complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q80TS3 · AlphaFold monomer V2.0 prediction for adhesion G protein-coupled receptor L3 (Q80TS3) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8BGT1 · AlphaFold monomer V2.0 prediction for leucine-rich repeat transmembrane protein FLRT3… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q80TS3
- Every structure of UniProt Q8BGT1
- Elsewhere: RCSB PDB 4YEB · PDBe 4YEB · UniProt Q80TS3 · UniProt Q8BGT1
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