Research workbench
Methionine adenosyltransferase complexed with ATP and a L-methionine analogue
Analyse Methionine adenosyltransferase complexed with ATP and a L-methionine analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O93
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine synthetase
- EC
- 2.5.1.6
- UniProt
- P13444
- Ligands
- LIS, ATP, MG, K, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | S-adenosylmethionine synthetase (EC 2.5.1.6) | protein | 368 | 27% helix, 24% strand | P13444 |
Ligands and binding sites
- LIS · (2S,4S)-2-amino-4,5-epoxipentanoic acid · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- K · Potassium 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.77 | 0.82 | 79 | K |
| 2 | 759 | 0.76 | 0.81 | 66 | LIS, PO4, MG, ATP, K |
| 3 | 470 | 0.71 | 0.81 | 43 | empty |
| 4 | 65 | 0.41 | 0.80 | 14 | empty |
| 5 | 59 | 0.40 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1820 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1O93 · Methionine Adenosyltransferase complexed with ATP and a L-methionine analogue · the same entry in another collection · chain A against A, TM-score 1.00
- P13444 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase isoform type-1… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P13444
- Elsewhere: RCSB PDB 1O93 · PDBe 1O93 · UniProt P13444
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