MolNFT v1 · #16778 · protein
Methionine adenosyltransferase complexed with ADP and a L-methionine analogue
1O92 · S-adenosylmethionine synthetase: “Methionine adenosyltransferase complexed with ADP and a L-methionine analogue”. X-ray diffraction, 5 ligands (AMB, ADP, MG), 4 pockets (best druggability 0.84). MolNFT v1 #16778 on GenesisL1: 3D…
- PDB
- 1O92
- 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
- AMB, ADP, MG, K, PO4
- Pockets
- 4 · best druggability 0.84
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
- AMB · L-2-amino-4-methoxy-cis-but-3-enoic acid · ligand · chains A
- ADP · Adenosine-5'-diphosphate · 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 · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.84 | 0.85 | 131 | AMB, PO4, MG, K |
| 2 | 432 | 0.72 | 0.82 | 37 | empty |
| 3 | 67 | 0.40 | 0.79 | 17 | empty |
| 4 | 59 | 0.38 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1807 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1O92 · Methionine Adenosyltransferase complexed with ADP 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 1O92 · PDBe 1O92 · UniProt P13444
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