MolNFT v1 · #96762 · protein
Mtordeltan-MLST8-PP242 complex
4JT5 · SERINE/THREONINE-protein kinase mtor: “Mtordeltan-MLST8-PP242 complex”. X-ray diffraction, 1 ligand (P2X), 20 pockets (best druggability 0.81). MolNFT v1 #96762 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JT5
- Type
- protein
- Length
- 2,746 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
- P2X
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 1058 | 66% helix, 5% strand | P42345 |
| D, C | Target of rapamycin complex subunit LST8 | protein | 317 | 0% helix, 51% strand | Q9BVC4 |
| A | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 1054 | 66% helix, 5% strand | P42345 |
Ligands and binding sites
- P2X · 2-[4-amino-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]-1H-indol-5-ol · ligand · 2 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.81 | 0.83 | 74 | empty |
| 2 | 917 | 0.81 | 0.83 | 74 | empty |
| 3 | 833 | 0.79 | 0.82 | 69 | empty |
| 4 | 937 | 0.77 | 0.80 | 70 | empty |
| 5 | 1017 | 0.77 | 0.79 | 86 | empty |
Interfaces
4 interfaces between chains.
- B–D · 944 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 937 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 695 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 145 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JT5 · mTORdeltaN-mLST8-pp242 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 A against A, TM-score 0.94
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 4JT5 · PDBe 4JT5 · UniProt P42345 · UniProt Q9BVC4
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