Research workbench
Structure of the plant like 5-aminolaevulinic acid dehydratase from chlorobium vibrioforme
Analyse Structure of the plant like 5-aminolaevulinic acid dehydratase from chlorobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W1Z
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta-aminolevulinic acid dehydratase
- EC
- 4.2.1.24
- UniProt
- Q59334
- Ligands
- SHF, MG
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 319 | 44% helix, 20% strand | Q59334 |
Ligands and binding sites
- SHF · Laevulinic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 415 | 0.66 | 0.79 | 53 | SHF |
| 2 | 300 | 0.65 | 0.81 | 52 | SHF |
| 3 | 60 | 0.47 | 0.84 | 16 | empty |
| 4 | 58 | 0.42 | 0.82 | 18 | empty |
| 5 | 77 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3047 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1W1Z · Structure of the plant like 5-Aminolaevulinic Acid Dehydratase from Chlorobium vibrioforme · the same entry in another collection · chain A against A, TM-score 1.00
- Q59334 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (Q59334) · 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 Q59334
- Elsewhere: RCSB PDB 1W1Z · PDBe 1W1Z · UniProt Q59334
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.