Research workbench
Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound
Analyse Insights into substrate and metal binding from the crystal structure of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PG1
- 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
- Y39, FE
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde decarbonylase (EC 4.1.99.5) | protein | 222 | 88% helix, 0% strand | Q7V6D4 |
Ligands and binding sites
- Y39 · (1S,2S)-2-nonylcyclopropanecarboxylic acid · ligand · 2 copies · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.81 | 0.96 | 31 | Y39, DMS |
| 2 | 146 | 0.53 | 0.80 | 22 | Y39 |
Compared structures
- 4PG1 · 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 0.98
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 4PG1 · PDBe 4PG1 · UniProt Q7V6D4
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