MolNFT v1 · #32800 · protein
5-(4-carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to porphobilinogen synthase from pseudomonas aeruginosa
2C15 · Delta-aminolevulinic acid dehydratase: “5-(4-carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to porphobilinogen synthase from pseudomonas…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.57). MolNFT v1…
- PDB
- 2C15
- Type
- protein
- Length
- 660 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
- Pockets
- 6 · best druggability 0.57
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 | 333 | 43% helix, 18% strand | Q59643 |
| B | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 327 | 45% helix, 18% strand | Q59643 |
Ligands and binding sites
- MG · Magnesium ion · metal · 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 | 117 | 0.57 | 0.84 | 16 | empty |
| 2 | 124 | 0.55 | 0.83 | 19 | empty |
| 3 | 331 | 0.55 | 0.75 | 50 | empty |
| 4 | 189 | 0.46 | 0.75 | 27 | empty |
| 5 | 57 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3542 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2C15 · 5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase… · 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 2C15 · PDBe 2C15 · UniProt Q59643
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