Research workbench
Cryo-EM structure of deptor bound to human mtor complex 1, dept-bound subset local refinement
Analyse Cryo-EM structure of deptor bound to human mtor complex 1, dept-bound subset… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PEC
- Type
- protein
- Length
- 3,878 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase mtor; Target of rapamycin complex subunit LST8…
- EC
- 2.7.11.1
- UniProt
- P42345, Q9BVC4, Q8N122, Q8TB45
- Ligands
- IHP
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2192 | 74% helix, 2% strand | P42345 |
| C | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 43% strand | Q9BVC4 |
| E | Regulatory-associated protein of mtor | protein | 1052 | 41% helix, 16% strand | Q8N122 |
| I | Dep domain-containing mtor-interacting protein | protein | 317 | 37% helix, 21% strand | Q8TB45 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
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 | 1098 | 0.81 | 0.83 | 74 | empty |
| 2 | 813 | 0.81 | 0.84 | 61 | empty |
| 3 | 1036 | 0.79 | 0.80 | 85 | empty |
| 4 | 986 | 0.78 | 0.80 | 84 | empty |
| 5 | 445 | 0.75 | 0.84 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–I · 2320 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 769 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7PEC · cryo-EM structure of DEPTOR bound to human mTOR complex 1, DEPt-bound subset local… · the same entry in another collection · chain I against I, 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 E 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 C against A, TM-score 0.97
- P42345 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase mtor (P42345) · a predicted model of the same protein · chain A against A, TM-score 0.87
- Q8TB45 · AlphaFold monomer V2.0 prediction for dep domain-containing mtor- interacting protein… · a predicted model of the same protein · chain I against A, TM-score 0.63
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 Q8N122
- Every structure of UniProt Q8TB45
- Elsewhere: RCSB PDB 7PEC · PDBe 7PEC · UniProt P42345 · UniProt Q9BVC4 · UniProt Q8N122 · UniProt Q8TB45
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