MolNFT v1 · #124091 · protein
Crystal structures of aldehyde deformylating oxygenase from oscillatoria sp. KNUA011
5K53: “Crystal structures of aldehyde deformylating oxygenase from oscillatoria sp. KNUA011”. X-ray diffraction, 2 ligands (STE, FE), 3 pockets (best druggability 0.82). MolNFT v1 #124091 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K53
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde deformylating oxygenase
- Ligands
- STE, FE
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde deformylating oxygenase | protein | 217 | 88% helix, 0% strand | — |
| B | Aldehyde deformylating oxygenase | protein | 219 | 87% helix, 0% strand | — |
Ligands and binding sites
- STE · Stearic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.82 | 0.97 | 32 | STE |
| 2 | 150 | 0.82 | 0.97 | 28 | STE |
| 3 | 532 | 0.66 | 0.77 | 68 | empty |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5K53 · Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011 · 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
- Elsewhere: RCSB PDB 5K53 · PDBe 5K53
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