MolNFT v1 · #53245 · protein
Porphobilinogen synthase (hemb) in complex with 5-acetamido-4- oxohexanoic acid (alaremycin 2)
2WOQ · Delta-aminolevulinic acid dehydratase: “Porphobilinogen synthase (hemb) in complex with 5-acetamido-4- oxohexanoic acid (alaremycin 2)”. X-ray diffraction, 2 ligands (AYC, MG), 3 pockets (best druggability 0.74). MolNFT v1 #53245 on…
- PDB
- 2WOQ
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- 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
- AYC, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) | protein | 328 | 44% helix, 18% strand | Q59643 |
Ligands and binding sites
- AYC · Alaremycin 2 · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 4 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.74 | 0.98 | 24 | AYC |
| 2 | 146 | 0.56 | 0.82 | 20 | empty |
| 3 | 60 | 0.31 | 0.75 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2WOQ · Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid… · 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 0.99
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 2WOQ · PDBe 2WOQ · UniProt Q59643
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