MolNFT v1 · #168521 · protein
Cryoem structure of the SLC38A9-raga-ragc-ragulator complex in the pre-gap state
6WJ2 · Ragulator complex protein LAMTOR1: “Cryoem structure of the SLC38A9-raga-ragc-ragulator complex in the pre-gap state”. Electron microscopy, 3 ligands (GDP, L8S, MG), 20 pockets (best druggability 0.79). MolNFT v1 #168521 on…
- PDB
- 6WJ2
- Type
- protein
- Length
- 1,167 residues
- Chains
- 8
- 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, Q8NBW4
- Ligands
- GDP, L8S, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 8 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ragulator complex protein LAMTOR1 | protein | 96 | 51% helix, 2% strand | Q6IAA8 |
| B | Ragulator complex protein LAMTOR2 | protein | 120 | 37% helix, 30% strand | Q9Y2Q5 |
| C | Ragulator complex protein LAMTOR3 | protein | 119 | 34% helix, 26% strand | Q9UHA4 |
| D | Ragulator complex protein LAMTOR4 | protein | 94 | 27% helix, 31% strand | Q0VGL1 |
| E | Ragulator complex protein LAMTOR5 | protein | 91 | 26% helix, 29% strand | A0A0C4DGV4 |
| F | RAS-related GTP-binding protein a | protein | 281 | 39% helix, 22% strand | Q7L523 |
| G | RAS-related GTP-binding protein C | protein | 308 | 38% helix, 19% strand | Q9HB90 |
| H | Sodium-coupled neutral amino acid transporter 9 | protein | 58 | 21% helix, 0% strand | Q8NBW4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains F, H
- 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
- MG · Magnesium ion · metal · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.79 | 0.82 | 92 | empty |
| 2 | 957 | 0.77 | 0.79 | 79 | empty |
| 3 | 794 | 0.73 | 0.78 | 75 | empty |
| 4 | 71 | 0.70 | 0.95 | 28 | empty |
| 5 | 189 | 0.66 | 0.85 | 34 | empty |
Interfaces
17 interfaces between chains.
- F–G · 1233 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1205 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1038 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 935 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 904 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WJ2 · CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state · the same entry in another collection · chain H against H, TM-score 1.00
- 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
- Q9Y2Q5 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR2 (Q9Y2Q5) · a predicted model of the same protein · chain B against A, TM-score 0.93
- 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 0.91
- Q0VGL1 · AlphaFold monomer V2.0 prediction for ragulator complex protein LAMTOR4 (Q0VGL1) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q8NBW4
- Elsewhere: RCSB PDB 6WJ2 · PDBe 6WJ2 · UniProt Q6IAA8 · UniProt Q9Y2Q5 · UniProt Q9UHA4 · UniProt Q0VGL1 · UniProt A0A0C4DGV4 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q8NBW4
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