MolNFT v1 · #163712 · protein
Cryo-EM structure of MTORC1 bound to active RAGA/C gtpases
6SB2 · MTOR,SERINE/THREONINE-protein kinase MTOR,MTOR…: “Cryo-EM structure of MTORC1 bound to active RAGA/C gtpases”. Electron microscopy, 2 ligands (GTP, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #163712 on GenesisL1: 3D…
- PDB
- 6SB2
- Type
- protein
- Length
- 8,235 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTOR,SERINE/THREONINE-protein kinase MTOR,MTOR, SERINE/THREONINE-protein kinase mtor…
- EC
- 2.7.11.1
- UniProt
- P42345, Q9BVC4, Q7L523, Q9HB90, Q8N122
- Ligands
- GTP, GDP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MTOR,SERINE/THREONINE-protein kinase MTOR,MTOR, SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2178 | 73% helix, 2% strand | P42345 |
| E, H | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 44% strand | Q9BVC4 |
| C, I | RAS-related GTP-binding protein a | protein | 298 | 41% helix, 26% strand | Q7L523 |
| D | RAS-related GTP-binding protein C | protein | 272 | 40% helix, 22% strand | Q9HB90 |
| Y, N | Regulatory-associated protein of mtor | protein | 1052 | 41% helix, 16% strand | Q8N122 |
| J | RAS-related GTP-binding protein C | protein | 273 | 41% helix, 21% strand | Q9HB90 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, I
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.86 | 0.87 | 161 | empty |
| 2 | 883 | 0.85 | 0.87 | 160 | empty |
| 3 | 864 | 0.84 | 0.86 | 135 | empty |
| 4 | 585 | 0.84 | 0.89 | 128 | empty |
| 5 | 803 | 0.83 | 0.86 | 122 | empty |
Interfaces
13 interfaces between chains.
- C–D · 719 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 699 Ų buried · 1 hydrogen bond · protein-protein
- I–J · 638 Ų buried · 8 hydrogen bonds · protein-protein
- A–Y · 596 Ų buried · 0 hydrogen bonds · protein-protein
- I–N · 573 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SB2 · cryo-EM structure of mTORC1 bound to active RagA/C GTPases · the same entry in another collection · chain N against N, TM-score 1.00
- Q8N122 · AlphaFold monomer V2.0 prediction for regulatory-associated protein of mtor (Q8N122) · a predicted model of the same protein · chain Y against A, TM-score 0.99
- Q9BVC4 · AlphaFold monomer V2.0 prediction for target of rapamycin complex subunit LST8 (Q9BVC4) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P42345
- Every structure of UniProt Q9BVC4
- Every structure of UniProt Q7L523
- Every structure of UniProt Q9HB90
- Every structure of UniProt Q8N122
- Elsewhere: RCSB PDB 6SB2 · PDBe 6SB2 · UniProt P42345 · UniProt Q9BVC4 · UniProt Q7L523 · UniProt Q9HB90 · UniProt Q8N122
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