Research workbench
Stepwise introduction of zinc binding site into porphobilinogen synthase of pseudomonas aeruginosa (mutations A129C and D139C)
Analyse Stepwise introduction of zinc binding site into porphobilinogen synthase of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W5M
- 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, CL
- 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 | 43% helix, 18% strand | Q59643 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 323 | 45% helix, 18% strand | Q59643 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.55 | 0.75 | 44 | empty |
| 2 | 111 | 0.54 | 0.83 | 15 | empty |
| 3 | 100 | 0.53 | 0.83 | 15 | empty |
| 4 | 206 | 0.49 | 0.76 | 30 | empty |
| 5 | 67 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3275 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 1W5M · Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas… · the same entry in another collection · chain B against B, 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 1W5M · PDBe 1W5M · UniProt Q59643
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