MolNFT v1 · #167179 · protein
Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 1 (ATMAT1) in complex with 5'-methylthioadenosine
6VCY: “Crystal structure of arabidopsis thaliana S-adenosylmethionine synthase 1 (ATMAT1) in complex with…”. X-ray diffraction, 4 ligands (MTA, MG, CL), 3 pockets (best druggability 0.43). MolNFT v1 #167179 on GenesisL1: 3D structure…
- PDB
- 6VCY
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.