Research workbench
Cryo-EM structure of human mtor complex 2, overall refinement
Analyse Cryo-EM structure of 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
- 6ZWM
- Type
- protein
- Length
- 7,437 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, Q6R327, Q9BPZ7
- Ligands
- AGS, IHP, ACE, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2184 | 65% helix, 2% strand | P42345 |
| B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2185 | 66% helix, 2% strand | P42345 |
| C, D | Target of rapamycin complex subunit LST8 | protein | 319 | 0% helix, 47% strand | Q9BVC4 |
| E, F | Rapamycin-insensitive companion of mtor | protein | 1117 | 61% helix, 1% strand | Q6R327 |
| G, 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 · 4 copies · chains A, B, E, F
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · 2 copies · chains E, G, F, H
- ZN · Zinc ion · metal · 2 copies · chains E, 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 | 1035 | 0.84 | 0.85 | 79 | empty |
| 2 | 846 | 0.82 | 0.84 | 67 | empty |
| 3 | 1086 | 0.81 | 0.82 | 94 | empty |
| 4 | 1047 | 0.81 | 0.82 | 98 | empty |
| 5 | 1144 | 0.80 | 0.81 | 103 | empty |
Interfaces
11 interfaces between chains.
- B–F · 3695 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 3598 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2339 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 2205 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 2201 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6ZWM · cryo-EM structure of human mTOR complex 2, overall refinement · 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 E 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 C 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 A against A, TM-score 0.88
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 6ZWM · PDBe 6ZWM · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7
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