MolNFT v1 · #13688 · protein
Crystal structure of L-threonine-O-3-phosphate decarboxylase from salmonella enterica
1LKC: “Crystal structure of L-threonine-O-3-phosphate decarboxylase from salmonella enterica”. X-ray diffraction, 2 ligands (PLP, PO4), 6 pockets (best druggability 0.65). MolNFT v1 #13688 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1LKC
- Type
- protein
- Length
- 355 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-threonine-O-3-phosphate decarboxylase
- UniProt
- P97084
- Ligands
- PLP, PO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-threonine-O-3-phosphate decarboxylase | protein | 355 | 42% helix, 16% strand | P97084 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.65 | 0.90 | 28 | EDO |
| 2 | 196 | 0.61 | 0.82 | 31 | PO4, PLP |
| 3 | 64 | 0.36 | 0.78 | 12 | empty |
| 4 | 51 | 0.35 | 0.79 | 14 | empty |
| 5 | 71 | 0.33 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1LKC · Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase from Salmonella enterica · the same entry in another collection · chain A against A, TM-score 1.00
- P97084 · AlphaFold monomer V2.0 prediction for threonine-phosphate decarboxylase (P97084) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P97084
- Elsewhere: RCSB PDB 1LKC · PDBe 1LKC · UniProt P97084
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