Research workbench
Structure of alas from S. cerevisiae non-covalently bound to plp cofactor
Analyse Structure of alas from S. cerevisiae non-covalently bound to plp cofactor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TXR
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-aminolevulinate synthase, mitochondrial
- EC
- 2.3.1.37
- UniProt
- P09950
- Ligands
- PLP, K
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 476 | 43% helix, 14% strand | P09950 |
| A | 5-aminolevulinate synthase, mitochondrial (EC 2.3.1.37) | protein | 479 | 43% helix, 14% strand | P09950 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains B, A
- K · Potassium ion · metal · chains A
- FMT · Formic acid · additive · 10 copies · chains B, A
- GOL · Glycerol · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.79 | 0.84 | 90 | FMT, PLP |
| 2 | 536 | 0.76 | 0.83 | 83 | FMT, PLP |
| 3 | 188 | 0.53 | 0.79 | 31 | empty |
| 4 | 167 | 0.48 | 0.77 | 27 | empty |
| 5 | 135 | 0.46 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- B–A · 4901 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 5TXR · Structure of ALAS from S. cerevisiae non-covalently bound to PLP cofactor · the same entry in another collection · chain B against B, TM-score 1.00
- P09950 · AlphaFold monomer V2.0 prediction for 5-aminolevulinate synthase, mitochondrial (P09950) · 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 P09950
- Elsewhere: RCSB PDB 5TXR · PDBe 5TXR · UniProt P09950
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