MolNFT v1 · #124090 · protein
Crystal structures of aldehyde deformylating oxygenase from limnothrix sp. KNUA012
5K52 · Aldehyde decarbonylase: “Crystal structures of aldehyde deformylating oxygenase from limnothrix sp. KNUA012”. X-ray diffraction, 1 ligand (OCD), 10 pockets (best druggability 0.84). MolNFT v1 #124090 on GenesisL1: 3D structure…
- PDB
- 5K52
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde decarbonylase
- EC
- 4.1.99.5
- UniProt
- A0A193CDY9
- Ligands
- OCD
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aldehyde decarbonylase (EC 4.1.99.5) | protein | 221 | 85% helix, 0% strand | A0A193CDY9 |
Ligands and binding sites
- OCD · octadecanal · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.84 | 0.85 | 109 | empty |
| 2 | 910 | 0.84 | 0.85 | 84 | empty |
| 3 | 160 | 0.82 | 0.97 | 30 | OCD |
| 4 | 154 | 0.82 | 0.98 | 31 | OCD |
| 5 | 116 | 0.80 | 0.98 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 866 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 853 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 450 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 408 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 260 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5K52 · Crystal structures of aldehyde deformylating oxygenase from Limnothrix sp. KNUA012 · 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 A0A193CDY9
- Elsewhere: RCSB PDB 5K52 · PDBe 5K52 · UniProt A0A193CDY9
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