Research workbench
Cryo-EM structure of human mtor complex 2, focused on one half
Analyse Cryo-EM structure of human mtor complex 2, focused on one half in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZWO
- Type
- protein
- Length
- 3,126 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, Q6R327, Q9BPZ7
- Ligands
- AGS, IHP, ACE, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 1592 | 64% helix, 3% strand | P42345 |
| D | Target of rapamycin complex subunit LST8 | protein | 319 | 0% helix, 47% strand | Q9BVC4 |
| F | Rapamycin-insensitive companion of mtor | protein | 1117 | 61% helix, 1% strand | Q6R327 |
| H | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 98 | 49% helix, 3% strand | Q9BPZ7 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains B, F
- IHP · Inositol hexakisphosphate · ligand · chains B
- ACE · Acetyl group · ligand · chains F, H
- ZN · Zinc ion · metal · chains F
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 | 946 | 0.83 | 0.85 | 80 | empty |
| 2 | 864 | 0.78 | 0.81 | 77 | empty |
| 3 | 876 | 0.77 | 0.80 | 62 | empty |
| 4 | 571 | 0.76 | 0.83 | 47 | empty |
| 5 | 388 | 0.71 | 0.83 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–F · 3610 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 2173 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 1294 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 927 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZWO · cryo-EM structure of human mTOR complex 2, focused on one half · the same entry in another collection · chain H against H, TM-score 1.00
- 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 0.96
- 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
- P42345 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase mtor (P42345) · a predicted model of the same protein · chain B against A, TM-score 0.89
- Q9BPZ7 · AlphaFold monomer V2.0 prediction for target of rapamycin complex 2 subunit MAPKAP1… · a predicted model of the same protein · chain H against A, TM-score 0.38
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
- Elsewhere: RCSB PDB 6ZWO · PDBe 6ZWO · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7
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