Research workbench
Cryo-EM structure of deptor bound to human mtor complex 2, overall refinement
Analyse Cryo-EM structure of deptor bound to human mtor complex 2, overall refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PE7
- Type
- protein
- Length
- 7,664 residues
- Chains
- 10
- 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, Q6R327, Q9BPZ7, Q8TB45
- Ligands
- IHP, ACE, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2194 | 68% helix, 2% strand | P42345 |
| D, C | Target of rapamycin complex subunit LST8 | protein | 319 | 0% helix, 45% strand | Q9BVC4 |
| F, E | Rapamycin-insensitive companion of mtor | protein | 1115 | 60% helix, 1% strand | Q6R327 |
| H, G | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 98 | 41% helix, 3% strand | Q9BPZ7 |
| I, J | 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
- ACE · Acetyl group · ligand · 2 copies · chains F, H, E, G
- ZN · Zinc ion · metal · 2 copies · chains F, E
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 | 1110 | 0.85 | 0.86 | 114 | empty |
| 2 | 899 | 0.82 | 0.84 | 77 | empty |
| 3 | 1014 | 0.82 | 0.83 | 77 | empty |
| 4 | 1075 | 0.82 | 0.83 | 104 | empty |
| 5 | 1096 | 0.79 | 0.80 | 71 | empty |
Interfaces
13 interfaces between chains.
- A–E · 3546 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 3540 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 2296 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 2291 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 2106 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7PE7 · cryo-EM structure of DEPTOR bound to human mTOR complex 2, overall refinement · the same entry in another collection · chain J against J, TM-score 1.00
- 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 0.96
- Q6R327 · AlphaFold monomer V2.0 prediction for rapamycin-insensitive companion of mtor (Q6R327) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q6R327
- Every structure of UniProt Q9BPZ7
- Every structure of UniProt Q8TB45
- Elsewhere: RCSB PDB 7PE7 · PDBe 7PE7 · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7 · UniProt Q8TB45
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