MolNFT v1 · #96763 · protein
Structure of mtordeltan-MLST8-pi-103 complex
4JT6: “Structure of mtordeltan-MLST8-pi-103 complex”. X-ray diffraction, 1 ligand (X6K), 20 pockets (best druggability 0.82). MolNFT v1 #96763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JT6
- Type
- protein
- Length
- 2,746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mtor; MLST8
- UniProt
- P42345, Q9BVC4
- Ligands
- X6K
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mtor | protein | 1058 | 66% helix, 4% strand | P42345 |
| D, C | MLST8 | protein | 317 | 0% helix, 51% strand | Q9BVC4 |
| A | Mtor | protein | 1054 | 67% helix, 4% strand | P42345 |
Ligands and binding sites
- X6K · 3-(4-morpholin-4-ylpyrido[3',2':4,5]furo[3,2-d]pyrimidin-2-yl)phenol · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.82 | 0.83 | 73 | empty |
| 2 | 946 | 0.82 | 0.83 | 74 | empty |
| 3 | 1074 | 0.80 | 0.81 | 105 | empty |
| 4 | 1071 | 0.80 | 0.81 | 101 | empty |
| 5 | 1166 | 0.78 | 0.79 | 83 | empty |
Interfaces
4 interfaces between chains.
- B–D · 953 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 673 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JT6 · structure of mTORDeltaN-mLST8-PI-103 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 0.97
- 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 0.94
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 4JT6 · PDBe 4JT6 · UniProt P42345 · UniProt Q9BVC4
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