Research workbench
Crystal structure of D. melanogaster samtor V66W/E67P mutant
Analyse Crystal structure of D. melanogaster samtor V66W/E67P mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VKK
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine sensor upstream of MTORC1
- EC
- 2.1.1.-
- UniProt
- Q9W138
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 287 | 45% helix, 22% strand | Q9W138 |
| B | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 234 | 36% helix, 27% strand | Q9W138 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.76 | 0.79 | 55 | empty |
| 2 | 204 | 0.61 | 0.81 | 40 | empty |
| 3 | 268 | 0.59 | 0.79 | 35 | empty |
| 4 | 215 | 0.58 | 0.80 | 35 | SO4 |
| 5 | 79 | 0.54 | 0.86 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2197 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7VKK · Crystal structure of D. melanogaster SAMTOR V66W/E67P mutant · the same entry in another collection · chain A against A, TM-score 1.00
- Q9W138 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine sensor upstream of MTORC1… · a predicted model of the same protein · chain B against A, TM-score 0.84
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 Q9W138
- Elsewhere: RCSB PDB 7VKK · PDBe 7VKK · UniProt Q9W138
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