MolNFT v1 · #96994 · protein
Crystal structure of S-adenosylmethionine synthetase from sulfolobus solfataricus complexed with SAM and ppi
4K0B · S-adenosylmethionine synthase: “Crystal structure of S-adenosylmethionine synthetase from sulfolobus solfataricus complexed with SAM and ppi”. X-ray diffraction, 4 ligands (DPO, SAM, MG), 9 pockets (best druggability 0.79). MolNFT…
- PDB
- 4K0B
- Type
- protein
- Length
- 805 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
- DPO, SAM, MG, PO4
- Pockets
- 9 · best druggability 0.79
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 | 401 | 36% helix, 31% strand | Q980S9 |
Ligands and binding sites
- DPO · Diphosphate · ligand · chains A, B
- SAM · S-adenosylmethionine · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.79 | 0.91 | 52 | MG, DPO, PO4, SAM |
| 2 | 816 | 0.74 | 0.79 | 78 | empty |
| 3 | 158 | 0.63 | 0.85 | 30 | empty |
| 4 | 185 | 0.47 | 0.75 | 33 | empty |
| 5 | 190 | 0.46 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2789 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4K0B · Crystal structure of S-Adenosylmethionine synthetase from Sulfolobus solfataricus… · the same entry in another collection · chain A against A, 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 4K0B · PDBe 4K0B · UniProt Q980S9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.