MolNFT v1 · #103429 · protein
Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate analogs bound
4PGI · Aldehyde decarbonylase: “Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating…”. X-ray diffraction, 2 ligands (Y69, FE), 1 pocket (best druggability 0.80). MolNFT v1 #103429…
- PDB
- 4PGI
- Type
- protein
- Length
- 222 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde decarbonylase
- EC
- 4.1.99.5
- UniProt
- Q7V6D4
- Ligands
- Y69, FE
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde decarbonylase (EC 4.1.99.5) | protein | 222 | 86% helix, 0% strand | Q7V6D4 |
Ligands and binding sites
- Y69 · 11-[2-(2-ethoxyethoxy)ethoxy]undecanal · ligand · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.80 | 0.93 | 40 | Y69 |
Compared structures
- 4PGI · Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7V6D4 · AlphaFold monomer V2.0 prediction for aldehyde decarbonylase (Q7V6D4) · 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 Q7V6D4
- Elsewhere: RCSB PDB 4PGI · PDBe 4PGI · UniProt Q7V6D4
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