MolNFT v1 · #32811 · protein
The X-ray structure of chlorobium vibrioforme 5- aminolaevulinic acid dehydratase complexed with a diacid inhibitor
2C1H · Delta-aminolevulinic acid dehydratase: “The X-ray structure of chlorobium vibrioforme 5- aminolaevulinic acid dehydratase complexed with a diacid…”. X-ray diffraction, 2 ligands (DSB, MG), 7 pockets (best druggability 0.68). MolNFT…
- PDB
- 2C1H
- 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
- DSB, MG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 319 | 45% helix, 17% strand | Q59334 |
Ligands and binding sites
- DSB · 4,7-dioxosebacic 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
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.68 | 0.97 | 19 | DSB |
| 2 | 226 | 0.50 | 0.75 | 34 | empty |
| 3 | 210 | 0.48 | 0.75 | 25 | empty |
| 4 | 52 | 0.47 | 0.85 | 16 | empty |
| 5 | 60 | 0.44 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3128 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2C1H · The X-ray Structure of Chlorobium vibrioforme 5-Aminolaevulinic Acid Dehydratase… · 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 2C1H · PDBe 2C1H · UniProt Q59334
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