Research workbench
High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase
Analyse High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B4K
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (5-aminolevulinic acid dehydratase)
- EC
- 4.2.1.24
- UniProt
- Q59643
- Ligands
- SHF, MG, SO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (5-aminolevulinic acid dehydratase) (EC 4.2.1.24) | protein | 326 | 45% helix, 18% strand | Q59643 |
| B | Protein (5-aminolevulinic acid dehydratase) (EC 4.2.1.24) | protein | 320 | 45% helix, 19% strand | Q59643 |
Ligands and binding sites
- SHF · Laevulinic acid · ligand · 2 copies · chains A, B
- MG · Magnesium 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.63 | 0.85 | 30 | SO4, SHF |
| 2 | 124 | 0.58 | 0.84 | 17 | empty |
| 3 | 136 | 0.56 | 0.82 | 19 | empty |
| 4 | 363 | 0.55 | 0.74 | 39 | empty |
| 5 | 132 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3030 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1B4K · High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase · the same entry in another collection · chain A against A, TM-score 1.00
- Q59643 · AlphaFold monomer V2.0 prediction for delta-aminolevulinic acid dehydratase (Q59643) · 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 Q59643
- Elsewhere: RCSB PDB 1B4K · PDBe 1B4K · UniProt Q59643
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