MolNFT v1 · #141600 · protein
4.9 ångström cryo-EM structure of human mtor complex 2
5ZCS · SERINE/THREONINE-protein kinase mtor: “4.9 ångström cryo-EM structure of human mtor complex 2”. Electron microscopy, 20 pockets (best druggability 0.90). MolNFT v1 #141600 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZCS
- Type
- protein
- Length
- 6,922 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
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 4 distinct chains · 46% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 2178 | 48% helix, 1% strand | P42345 |
| C, D | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 36% strand | Q9BVC4 |
| E, F | Rapamycin-insensitive companion of mtor | protein | 880 | 60% helix, 0% strand | Q6R327 |
| G, H | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 86 | 48% helix, 0% strand | Q9BPZ7 |
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 | 1123 | 0.90 | 0.92 | 140 | empty |
| 2 | 740 | 0.89 | 0.92 | 92 | empty |
| 3 | 710 | 0.89 | 0.92 | 83 | empty |
| 4 | 1184 | 0.88 | 0.89 | 123 | empty |
| 5 | 545 | 0.86 | 0.92 | 76 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2192 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 874 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 821 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 628 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 588 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ZCS · 4.9 Angstrom Cryo-EM structure of human mTOR complex 2 · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.92
- 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 0.85
- 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 0.40
- Q9BPZ7 · AlphaFold monomer V2.0 prediction for target of rapamycin complex 2 subunit MAPKAP1… · a predicted model of the same protein · chain G against A, TM-score 0.40
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 5ZCS · PDBe 5ZCS · UniProt P42345 · UniProt Q9BVC4 · UniProt Q6R327 · UniProt Q9BPZ7
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