Research workbench
Structure of mtordeltan-MLST8-atpgammas-mg complex
Analyse Structure of mtordeltan-MLST8-atpgammas-mg complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JSP
- Type
- protein
- Length
- 2,750 residues
- Chains
- 4
- Method
- x-ray diffraction
- 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
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 1058 | 67% helix, 4% strand | P42345 |
| D, C | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 51% strand | Q9BVC4 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 4 copies · chains B, A
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 | 781 | 0.81 | 0.84 | 61 | empty |
| 2 | 751 | 0.81 | 0.84 | 60 | empty |
| 3 | 1095 | 0.79 | 0.80 | 69 | empty |
| 4 | 982 | 0.78 | 0.80 | 66 | empty |
| 5 | 714 | 0.76 | 0.81 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–D · 938 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 720 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4JSP · structure of mTORDeltaN-mLST8-ATPgammaS-Mg complex · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.98
- 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 0.93
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
- Elsewhere: RCSB PDB 4JSP · PDBe 4JSP · UniProt P42345 · UniProt Q9BVC4
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