Research workbench
Crystal structure of S-adenosylmethionine synthase from sulfolobus solfataricus complexed with SAM and ppi
Analyse Crystal structure of S-adenosylmethionine synthase from sulfolobus solfataricus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L7I
- Type
- protein
- Length
- 801 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthase
- EC
- 2.5.1.6
- UniProt
- Q980S9
- Ligands
- SAM, DPO, MG, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 404 | 36% helix, 29% strand | Q980S9 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 397 | 35% helix, 31% strand | Q980S9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A, B
- DPO · Diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.78 | 0.88 | 65 | MG, SAM, PO4, DPO |
| 2 | 818 | 0.75 | 0.80 | 73 | PO4 |
| 3 | 170 | 0.60 | 0.83 | 29 | empty |
| 4 | 231 | 0.51 | 0.76 | 28 | empty |
| 5 | 196 | 0.51 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2766 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4L7I · Crystal structure of S-Adenosylmethionine synthase from Sulfolobus solfataricus complexed… · the same entry in another collection · chain B against B, TM-score 1.00
- Q980S9 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q980S9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q980S9
- Elsewhere: RCSB PDB 4L7I · PDBe 4L7I · UniProt Q980S9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.