Research workbench
Cryo-EM structure of saccharomyces cerevisiae target of rapamycin complex 2
Analyse Cryo-EM structure of saccharomyces cerevisiae target of rapamycin complex 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EMK
- Type
- protein
- Length
- 6,332 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase TOR2; Target of rapamycin complex subunit LST8; Target of…
- EC
- 2.7.1.67, 2.7.11.1
- UniProt
- P32600, P41318, Q04749, Q08236
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 5 distinct chains · 7% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SERINE/THREONINE-protein kinase TOR2 (EC 2.7.1.67, 2.7.11.1) | protein | 2262 | 9% helix, 1% strand | P32600 |
| B, D | Target of rapamycin complex subunit LST8 | protein | 300 | 0% helix, 5% strand | P41318 |
| E, F | Target of rapamycin complex 2 subunit TSC11 | protein | 303 | 5% helix, 0% strand | — |
| G, H | Target of rapamycin complex 2 subunit AVO2 | protein | 155 | 5% helix, 0% strand | Q04749 |
| I, J | Target of rapamycin complex 2 subunit AVO1 | protein | 146 | 0% helix, 1% strand | Q08236 |
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 | 590 | 0.90 | 0.95 | 83 | empty |
| 2 | 583 | 0.90 | 0.95 | 86 | empty |
| 3 | 1186 | 0.86 | 0.87 | 130 | empty |
| 4 | 289 | 0.85 | 0.96 | 55 | empty |
| 5 | 825 | 0.84 | 0.86 | 100 | empty |
Interfaces
14 interfaces between chains.
- A–C · 2415 Ų buried · 21 hydrogen bonds · protein-protein
- C–J · 979 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 15 hydrogen bonds · protein-protein
- A–I · 845 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 828 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6EMK · Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2 · the same entry in another collection · chain J against J, TM-score 1.00
- P41318 · AlphaFold monomer V2.0 prediction for target of rapamycin complex subunit LST8 (P41318) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q04749 · AlphaFold monomer V2.0 prediction for target of rapamycin complex 2 subunit AVO2 (Q04749) · a predicted model of the same protein · chain G against A, TM-score 0.83
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 P32600
- Every structure of UniProt P41318
- Every structure of UniProt Q04749
- Every structure of UniProt Q08236
- Elsewhere: RCSB PDB 6EMK · PDBe 6EMK · UniProt P32600 · UniProt P41318 · UniProt Q04749 · UniProt Q08236
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