MolNFT v1 · #115532 · protein
FLRT3 lrr domain in complex with LPHN3 olfactomedin domain
5CMN · Leucine-rich repeat transmembrane protein FLRT3: “FLRT3 lrr domain in complex with LPHN3 olfactomedin domain”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.84). MolNFT v1 #115532 on GenesisL1: 3D…
- PDB
- 5CMN
- Type
- protein
- Length
- 2,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat transmembrane protein FLRT3; Latrophilin-3
- UniProt
- Q9NZU0, Q9HAR2
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Leucine-rich repeat transmembrane protein FLRT3 | protein | 321 | 12% helix, 16% strand | Q9NZU0 |
| E, F, G, H | Latrophilin-3 | protein | 247 | 2% helix, 52% strand | Q9HAR2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.84 | 0.88 | 73 | empty |
| 2 | 1101 | 0.82 | 0.83 | 81 | empty |
| 3 | 1125 | 0.79 | 0.81 | 101 | empty |
| 4 | 475 | 0.74 | 0.83 | 53 | empty |
| 5 | 962 | 0.73 | 0.77 | 94 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1525 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1492 Ų buried · 33 hydrogen bonds · protein-protein
- C–G · 902 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 833 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 820 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5CMN · FLRT3 LRR domain in complex with LPHN3 Olfactomedin domain · the same entry in another collection · chain H against H, TM-score 1.00
- Q9HAR2 · AlphaFold monomer V2.0 prediction for adhesion G protein-coupled receptor L3 (Q9HAR2) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q9NZU0 · AlphaFold monomer V2.0 prediction for leucine-rich repeat transmembrane protein FLRT3… · 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 Q9NZU0
- Every structure of UniProt Q9HAR2
- Elsewhere: RCSB PDB 5CMN · PDBe 5CMN · UniProt Q9NZU0 · UniProt Q9HAR2
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