MolNFT v1 · #25790 · protein
Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations A129C, D131C, D139C, P132E)
1W5P · Delta-aminolevulinic acid dehydratase: “Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations…”. X-ray diffraction, 4 ligands (K, MG, ZN), 9 pockets (best druggability 0.64).…
- PDB
- 1W5P
- Type
- protein
- Length
- 642 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, SO4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 321 | 45% 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
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.64 | 0.86 | 31 | FMT |
| 2 | 115 | 0.64 | 0.88 | 22 | FMT |
| 3 | 152 | 0.55 | 0.81 | 20 | GOL |
| 4 | 106 | 0.54 | 0.83 | 16 | GOL |
| 5 | 145 | 0.41 | 0.74 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 3186 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 1W5P · Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas… · 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 1W5P · PDBe 1W5P · UniProt Q59643
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