MolNFT v1 · #119362 · protein
Tetrameric complex of latrophilin 3, UNC5D and FLRT2
5FTU · Netrin receptor UNC5D: “Tetrameric complex of latrophilin 3, UNC5D and FLRT2”. X-ray diffraction, 3 ligands (NAG, NA, CA), 20 pockets (best druggability 0.84). MolNFT v1 #119362 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5FTU
- Type
- protein
- Length
- 3,180 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin receptor UNC5D; Leucine-rich repeat transmembrane protein FLRT2; Adhesion G…
- UniProt
- F1LW30, Q8BLU0, Q80TS3
- Ligands
- NAG, NA, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Netrin receptor UNC5D | protein | 106 | 5% helix, 42% strand | F1LW30 |
| B, F, J | Leucine-rich repeat transmembrane protein FLRT2 | protein | 326 | 6% helix, 16% strand | Q8BLU0 |
| C, G, K | Adhesion G protein-coupled receptor L3 | protein | 365 | 5% helix, 42% strand | Q80TS3 |
| D, H, L | Adhesion G protein-coupled receptor L3 | protein | 263 | 2% helix, 47% strand | Q80TS3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, E, F, G, I, J, K
- NA · Sodium ion · metal · 6 copies · chains C, D, G, H, K, L
- CA · Calcium ion · metal · 6 copies · chains C, D, G, H, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.84 | 0.85 | 86 | NAG |
| 2 | 884 | 0.84 | 0.86 | 91 | NAG |
| 3 | 1138 | 0.82 | 0.83 | 98 | NAG |
| 4 | 1001 | 0.81 | 0.82 | 86 | empty |
| 5 | 962 | 0.81 | 0.82 | 90 | empty |
Interfaces
21 interfaces between chains.
- B–C · 986 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 973 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 972 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 795 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 789 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FTU · Tetrameric complex of Latrophilin 3, Unc5D and FLRT2 · the same entry in another collection · chain L against L, 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 F1LW30
- Every structure of UniProt Q8BLU0
- Every structure of UniProt Q80TS3
- Elsewhere: RCSB PDB 5FTU · PDBe 5FTU · UniProt F1LW30 · UniProt Q8BLU0 · UniProt Q80TS3
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