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Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1 (AtMAT1) in complex with 5'-methylthioadenosine
Analyse Crystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VCY
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Arabidopsis thaliana
- Molecule
- S-adenosylmethionine synthase 1
- EC
- 2.5.1.6
- UniProt
- P23686
- Ligands
- MTA, MG, CL, SO4
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · resolution 1.82 · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase 1 (EC 2.5.1.6) | protein | 385 | 30% helix, 26% strand | P23686 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 7 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.43 | 0.76 | 26 | empty |
| 2 | 50 | 0.31 | 0.77 | 18 | empty |
| 3 | 70 | 0.30 | 0.74 | 22 | CL |
Compared structures
- 6VCY · Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 1 (ATMAT1) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P23686 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase 1 (P23686) · a predicted model of the same protein · chain A 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 P23686
- Elsewhere: RCSB PDB 6VCY · PDBe 6VCY · UniProt P23686
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