Research workbench
Crystal structure of D. melanogaster samtor in complex with SAM
Analyse Crystal structure of D. melanogaster samtor in complex with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VKR
- Type
- protein
- Length
- 855 residues
- Chains
- 4
- 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
- SAM
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 221 | 36% helix, 29% strand | Q9W138 |
| B | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 220 | 34% helix, 29% strand | Q9W138 |
| C | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 205 | 38% helix, 31% strand | Q9W138 |
| D | S-adenosylmethionine sensor upstream of MTORC1 (EC 2.1.1.-) | protein | 209 | 37% helix, 30% strand | Q9W138 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.78 | 0.80 | 100 | empty |
| 2 | 974 | 0.77 | 0.79 | 70 | CIT |
| 3 | 329 | 0.61 | 0.78 | 36 | empty |
| 4 | 348 | 0.59 | 0.77 | 30 | CIT |
| 5 | 111 | 0.49 | 0.80 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 831 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 350 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 146 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 7VKR · Crystal structure of D. melanogaster SAMTOR in complex with SAM · the same entry in another collection · chain D against D, 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 0.99
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 7VKR · PDBe 7VKR · UniProt Q9W138
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