Research workbench
Cryo-EM structure of deptor bound to human mtor complex 1, overall refinement
Analyse Cryo-EM structure of deptor bound to human mtor complex 1, overall refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PEA
- Type
- protein
- Length
- 7,334 residues
- Chains
- 8
- 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 0.86
Structure
electron microscopy · 4 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2192 | 74% helix, 2% strand | P42345 |
| D, C | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 43% strand | Q9BVC4 |
| F, E | Regulatory-associated protein of mtor | protein | 1052 | 41% helix, 17% strand | Q8N122 |
| J, I | Dep domain-containing mtor-interacting protein | protein | 106 | 13% helix, 25% strand | Q8TB45 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains B, 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 | 1079 | 0.86 | 0.87 | 102 | empty |
| 2 | 1077 | 0.85 | 0.86 | 101 | empty |
| 3 | 838 | 0.82 | 0.84 | 64 | empty |
| 4 | 842 | 0.81 | 0.84 | 62 | empty |
| 5 | 1161 | 0.80 | 0.81 | 70 | empty |
Interfaces
9 interfaces between chains.
- B–A · 2048 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1375 Ų buried · 5 hydrogen bonds · protein-protein
- B–J · 1229 Ų buried · 16 hydrogen bonds · protein-protein
- A–I · 1223 Ų buried · 16 hydrogen bonds · protein-protein
- F–A · 1209 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7PEA · cryo-EM structure of DEPTOR bound to human mTOR complex 1, overall refinement · 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 F 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 D against A, TM-score 0.98
- Q8TB45 · AlphaFold monomer V2.0 prediction for dep domain-containing mtor- interacting protein… · a predicted model of the same protein · chain J against A, TM-score 0.91
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 7PEA · PDBe 7PEA · UniProt P42345 · UniProt Q9BVC4 · UniProt Q8N122 · UniProt Q8TB45
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