Research workbench
5-hydroxy-levulinic acid bound to porphobilinogen synthase from pseudomonas aeruginosa
Analyse 5-hydroxy-levulinic acid bound to porphobilinogen synthase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C13
- Type
- protein
- Length
- 663 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, K, CL
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 330 | 43% helix, 18% strand | Q59643 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 119 | 0.55 | 0.83 | 17 | empty |
| 2 | 131 | 0.55 | 0.82 | 16 | empty |
| 3 | 312 | 0.55 | 0.75 | 41 | PGE |
| 4 | 203 | 0.47 | 0.74 | 24 | empty |
| 5 | 56 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3561 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2C13 · 5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa · 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 2C13 · PDBe 2C13 · UniProt Q59643
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