Research workbench
Crystal structure of S-adenosylmethionine decarboxylase from potato
Analyse Crystal structure of S-adenosylmethionine decarboxylase from potato in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MHM
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase
- EC
- 4.1.1.50
- UniProt
- Q04694
- Ligands
- PYR
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase (EC 4.1.1.50) | protein | 54 | 26% helix, 39% strand | Q04694 |
| A | S-adenosylmethionine decarboxylase (EC 4.1.1.50) | protein | 253 | 26% helix, 39% strand | Q04694 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.64 | 0.79 | 40 | empty |
| 2 | 152 | 0.50 | 0.79 | 21 | PYR |
| 3 | 85 | 0.48 | 0.82 | 28 | empty |
Interfaces
1 interface between chains.
- B–A · 2650 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1MHM · Crystal structure of S-adenosylmethionine decarboxylase from potato · the same entry in another collection · chain B against B, TM-score 1.00
- Q04694 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q04694
- Elsewhere: RCSB PDB 1MHM · PDBe 1MHM · UniProt Q04694
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