MolNFT v1 · #11383 · protein
Structure of a human S-adenosylmethionine decarboxylase self- processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant
1JL0 · S-adenosylmethionine decarboxylase proenzyme: “Structure of a human S-adenosylmethionine decarboxylase self- processing ester intermediate and mechanism of…”. X-ray diffraction, 1 ligand (PUT), 9 pockets (best druggability 0.65).…
- PDB
- 1JL0
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase proenzyme
- EC
- 4.1.1.50
- UniProt
- P17707
- Ligands
- PUT
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 310 | 21% helix, 38% strand | P17707 |
| B | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 311 | 23% helix, 39% strand | P17707 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.65 | 0.91 | 25 | empty |
| 2 | 97 | 0.51 | 0.82 | 22 | TRS |
| 3 | 100 | 0.49 | 0.82 | 23 | TRS |
| 4 | 103 | 0.49 | 0.81 | 23 | empty |
| 5 | 152 | 0.43 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1057 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1JL0 · Structure of a Human S-Adenosylmethionine Decarboxylase Self-processing Ester… · the same entry in another collection · chain A against A, TM-score 1.00
- P17707 · 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 P17707
- Elsewhere: RCSB PDB 1JL0 · PDBe 1JL0 · UniProt P17707
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