Research workbench
Structure of a S-adenosylmethionine synthetase from mycobacterium avium
Analyse Structure of a S-adenosylmethionine synthetase from mycobacterium avium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S82
- Type
- protein
- Length
- 749 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
- A0QI26
- Ligands
- CA, UNL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 373 | 34% helix, 26% strand | A0QI26 |
| B | S-adenosylmethionine synthase (EC 2.5.1.6) | protein | 376 | 34% helix, 26% strand | A0QI26 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- UNL · Unknown ligand · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.73 | 0.81 | 44 | GOL |
| 2 | 670 | 0.72 | 0.79 | 74 | UNL |
| 3 | 590 | 0.69 | 0.78 | 59 | UNL |
| 4 | 122 | 0.42 | 0.76 | 24 | empty |
| 5 | 95 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2182 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3S82 · Structure of a S-adenosylmethionine synthetase from Mycobacterium avium · the same entry in another collection · chain A against A, TM-score 1.00
- A0QI26 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (A0QI26) · a predicted model of the same protein · chain A 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 A0QI26
- Elsewhere: RCSB PDB 3S82 · PDBe 3S82 · UniProt A0QI26
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