Research workbench
CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused region of mTOR and RAPTOR on one protomer copy.
Analyse CryoEM structure of mTORC1 with a paediatric kidney cancer-associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8RCN
- Type
- protein
- Length
- 1,854 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens
- Molecule
- Serine/threonine-protein kinase mTOR; Regulatory-associated protein of mTOR; Eukaryotic…
- EC
- 2.7.11.1
- UniProt
- P42345, Q8N122, Q13541
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · resolution 3.1 · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Serine/threonine-protein kinase mTOR (EC 2.7.11.1) | protein | 1521 | 71% helix, 3% strand | P42345 |
| Y | Regulatory-associated protein of mTOR | protein | 325 | 45% helix, 10% strand | Q8N122 |
| X | Eukaryotic translation initiation factor 4E-binding protein 1 | protein | 8 | 0% helix, 0% strand | Q13541 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.77 | 0.96 | 28 | empty |
| 2 | 302 | 0.77 | 0.88 | 48 | empty |
| 3 | 702 | 0.76 | 0.81 | 64 | empty |
| 4 | 631 | 0.75 | 0.81 | 47 | empty |
| 5 | 147 | 0.73 | 0.92 | 34 | empty |
Interfaces
2 interfaces between chains.
- B–Y · 805 Ų buried · 5 hydrogen bonds · protein-protein
- Y–X · 337 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- Q8N122 · AlphaFold monomer V2.0 prediction for regulatory-associated protein of mtor (Q8N122) · a predicted model of the same protein · chain Y 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 0.91
- Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain X against A, TM-score 0.32
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 Q8N122
- Every structure of UniProt Q13541
- Elsewhere: RCSB PDB 8RCN · PDBe 8RCN · UniProt P42345 · UniProt Q8N122 · UniProt Q13541
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