MolNFT v1 · #25788 · protein
Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations D131C and D139C)
1W5N · Delta-aminolevulinic acid dehydratase: “Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations…”. X-ray diffraction, 4 ligands (MG, ZN, NA), 9 pockets (best druggability 0.72).…
- PDB
- 1W5N
- Type
- protein
- Length
- 645 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, NA, CL
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 322 | 45% helix, 18% strand | Q59643 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 323 | 46% 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
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.72 | 0.95 | 26 | FMT, ZN |
| 2 | 71 | 0.68 | 0.94 | 21 | empty |
| 3 | 107 | 0.56 | 0.84 | 15 | empty |
| 4 | 123 | 0.53 | 0.81 | 16 | empty |
| 5 | 224 | 0.51 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 3265 Ų buried · 78 hydrogen bonds · protein-protein
Compared structures
- 1W5N · 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 1W5N · PDBe 1W5N · UniProt Q59643
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