Research workbench
Protein 84 with aldehyde deformylating oxygenase activity from sulfolobus tokodaii (orthorhombic form)
Analyse Protein 84 with aldehyde deformylating oxygenase activity from sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V4T
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetic aldehyde deformylating oxygenase
- UniProt
- Q970H5
- Ligands
- FE
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetic aldehyde deformylating oxygenase | protein | 212 | 81% helix, 0% strand | Q970H5 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
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 | 477 | 0.85 | 0.91 | 53 | empty |
| 2 | 476 | 0.84 | 0.90 | 51 | empty |
| 3 | 125 | 0.43 | 0.76 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5V4T · Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii… · the same entry in another collection · 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 Q970H5
- Elsewhere: RCSB PDB 5V4T · PDBe 5V4T · UniProt Q970H5
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