MolNFT v1 · #17072 · protein
Yeast 5-aminolaevulinic acid dehydratase putative cyclic reaction intermediate complex
1OHL · Delta-aminolevulinic acid dehydratase: “Yeast 5-aminolaevulinic acid dehydratase putative cyclic reaction intermediate complex”. X-ray diffraction, 2 ligands (PBG, ZN), 3 pockets (best druggability 0.32). MolNFT v1 #17072 on…
- PDB
- 1OHL
- Type
- protein
- Length
- 340 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-aminolevulinic acid dehydratase
- EC
- 4.2.1.24
- UniProt
- P05373
- Ligands
- PBG, ZN
- Pockets
- 3 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 340 | 40% helix, 17% strand | P05373 |
Ligands and binding sites
- PBG · 3-[5-(aminomethyl)-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- BME · Beta-mercaptoethanol · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.32 | 0.76 | 13 | empty |
| 2 | 67 | 0.30 | 0.74 | 15 | empty |
| 3 | 55 | 0.28 | 0.74 | 14 | empty |
Modifications
Observed in the structure: 2 covalent (additive adduct, covalent ligand).
Compared structures
- 1OHL · Yeast 5-aminolaevulinic acid dehydratase putative cyclic reaction intermediate complex · the same entry in another collection · chain A against A, TM-score 1.00
- P05373 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (P05373) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P05373
- Elsewhere: RCSB PDB 1OHL · PDBe 1OHL · UniProt P05373
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