Research workbench
The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase.
Analyse The X-ray structure of octameric human native 5-aminolaevulinic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HNR
- Type
- protein
- Length
- 624 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
- P13716
- Ligands
- DAV, ZN, SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 326 | 41% helix, 17% strand | P13716 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 298 | 43% helix, 17% strand | P13716 |
Ligands and binding sites
- DAV · Delta-amino valeric acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.72 | 0.97 | 22 | DAV |
| 2 | 192 | 0.60 | 0.82 | 26 | empty |
| 3 | 204 | 0.46 | 0.74 | 22 | empty |
| 4 | 175 | 0.43 | 0.73 | 21 | SO4 |
| 5 | 116 | 0.40 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2914 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HNR · The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase. · the same entry in another collection · chain A against A, TM-score 1.00
- P13716 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (P13716) · 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 P13716
- Elsewhere: RCSB PDB 5HNR · PDBe 5HNR · UniProt P13716
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.