Research workbench
Stepwise introduction of a zinc binding site into porphobilinogen synthase from pseudomonas aeruginosa (mutation D139C)
Analyse Stepwise introduction of a zinc binding site into porphobilinogen synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W54
- Type
- protein
- Length
- 632 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
- Q59643
- Ligands
- K, MG, ZN
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 311 | 46% helix, 19% strand | Q59643 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 321 | 44% helix, 18% strand | Q59643 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 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 | 170 | 0.64 | 0.85 | 28 | FMT |
| 2 | 159 | 0.56 | 0.81 | 29 | FMT |
| 3 | 116 | 0.55 | 0.83 | 15 | empty |
| 4 | 118 | 0.55 | 0.82 | 19 | empty |
| 5 | 137 | 0.40 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3128 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 1W54 · Stepwise introduction of a zinc binding site into Porphobilinogen synthase from… · 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 1W54 · PDBe 1W54 · UniProt Q59643
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.