Research workbench
X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid
Analyse X-ray structure of 5-aminolevulinic acid dehydratase complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B4E
- Type
- protein
- Length
- 323 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (5-aminolevulinic acid dehydratase)
- EC
- 4.2.1.24
- UniProt
- P0ACB2
- Ligands
- SHF, ZN, SO4
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (5-aminolevulinic acid dehydratase) (EC 4.2.1.24) | protein | 323 | 43% helix, 17% strand | P0ACB2 |
Ligands and binding sites
- SHF · Laevulinic acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.58 | 0.83 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1B4E · X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACB2 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (P0ACB2) · 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 P0ACB2
- Elsewhere: RCSB PDB 1B4E · PDBe 1B4E · UniProt P0ACB2
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