MolNFT v1 · #98224 · protein
Crystal structure of S-adenosylmethionine synthetase from sulfolobus solfataricus complexed with sae and ppi
4L2Z · S-adenosylmethionine synthase: “Crystal structure of S-adenosylmethionine synthetase from sulfolobus solfataricus complexed with sae and ppi”. X-ray diffraction, 4 ligands (S7M, DPO, MG), 9 pockets (best druggability 0.81). MolNFT…
- PDB
- 4L2Z
- 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
- S7M, DPO, MG, PO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 404 | 35% helix, 29% strand | Q980S9 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 397 | 35% helix, 31% strand | Q980S9 |
Ligands and binding sites
- S7M · [(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}ethyls ulfonium · ligand · chains A, B
- DPO · Diphosphate · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.81 | 0.91 | 63 | MG, S7M, DPO, PO4 |
| 2 | 854 | 0.75 | 0.79 | 78 | empty |
| 3 | 289 | 0.73 | 0.86 | 40 | empty |
| 4 | 50 | 0.69 | 0.98 | 25 | empty |
| 5 | 220 | 0.51 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2768 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4L2Z · 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 4L2Z · PDBe 4L2Z · UniProt Q980S9
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