Research workbench
Cryo-EM structure of the lysosomal folliculin complex (flcn-FNIP2- raga-ragc-ragulator)
Analyse Cryo-EM structure of the lysosomal folliculin complex (flcn-FNIP2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NZD
- Type
- protein
- Length
- 1,810 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ragulator complex protein LAMTOR1; Ragulator complex protein LAMTOR2; Ragulator complex…
- UniProt
- Q6IAA8, Q9Y2Q5, Q9UHA4, Q0VGL1, A0A0C4DGV4, Q7L523, Q9HB90, Q8NFG4, Q9P278
- Ligands
- GDP, L8S
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR1 | protein | 81 | 58% helix, 1% strand | Q6IAA8 |
| B | Ragulator complex protein LAMTOR2 | protein | 126 | 40% helix, 28% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR3 | protein | 121 | 40% helix, 30% strand | Q9UHA4 |
| D | Ragulator complex protein LAMTOR4 | protein | 90 | 26% helix, 40% strand | Q0VGL1 |
| E | Hepatitis B virus X interacting protein | protein | 91 | 31% helix, 37% strand | A0A0C4DGV4 |
| F | RAS-related GTP-binding protein a | protein | 227 | 43% helix, 23% strand | Q7L523 |
| G | RAS-related GTP-binding protein C | protein | 299 | 41% helix, 19% strand | Q9HB90 |
| H | Folliculin | protein | 387 | 43% helix, 16% strand | Q8NFG4 |
| I | Folliculin-interacting protein 2 | protein | 388 | 48% helix, 12% strand | Q9P278 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains F, H, I
- L8S · 9-{5-O-[(S)-hydroxy{[(r)-hydroxy(thiophosphonooxy) phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione · ligand · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.83 | 122 | empty |
| 2 | 1045 | 0.81 | 0.82 | 109 | empty |
| 3 | 800 | 0.78 | 0.81 | 82 | empty |
| 4 | 960 | 0.78 | 0.80 | 96 | GDP |
| 5 | 392 | 0.73 | 0.84 | 42 | L8S |
Interfaces
20 interfaces between chains.
- H–I · 1818 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1336 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1243 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1052 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 982 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NZD · Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator) · the same entry in another collection · chain I against I, TM-score 1.00
- Q9UHA4 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR3 (Q9UHA4) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9HB90 · AlphaFold monomer V2.0 prediction for RAS-related GTP-binding protein C (Q9HB90) · a predicted model of the same protein · chain G against A, TM-score 0.97
- Q9P278 · AlphaFold monomer V2.0 prediction for folliculin-interacting protein 2 (Q9P278) · a predicted model of the same protein · chain I against A, TM-score 0.96
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 Q6IAA8
- Every structure of UniProt Q9Y2Q5
- Every structure of UniProt Q9UHA4
- Every structure of UniProt Q0VGL1
- Every structure of UniProt A0A0C4DGV4
- Every structure of UniProt Q7L523
- Every structure of UniProt Q9HB90
- Every structure of UniProt Q8NFG4
- Every structure of UniProt Q9P278
- Elsewhere: RCSB PDB 6NZD · PDBe 6NZD · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt A0A0C4DGV4 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q8NFG4 · UniProt Q9P278
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