MolNFT v1 · #25771 · protein
Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations A129C and D131C)
1W56 · Delta-aminolevulinic acid dehydratase: “Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations…”. X-ray diffraction, 3 ligands (MG, ZN, K), 6 pockets (best druggability 0.55).…
- PDB
- 1W56
- Type
- protein
- Length
- 652 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
- MG, ZN, K
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 329 | 45% helix, 18% strand | Q59643 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 323 | 43% helix, 18% strand | Q59643 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium 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
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.55 | 0.81 | 21 | empty |
| 2 | 128 | 0.55 | 0.82 | 16 | empty |
| 3 | 302 | 0.53 | 0.75 | 41 | empty |
| 4 | 227 | 0.51 | 0.76 | 36 | empty |
| 5 | 59 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3244 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 1W56 · 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 1W56 · PDBe 1W56 · UniProt Q59643
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