Research workbench
Crystal structure of cholesterol oxidase from B.STEROLICUM
Analyse Crystal structure of cholesterol oxidase from B.STEROLICUM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I19
- Type
- protein
- Length
- 1,079 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholesterol oxidase
- EC
- 1.1.3.6
- UniProt
- Q7SID9
- Ligands
- FAD, MN
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholesterol oxidase (EC 1.1.3.6) | protein | 541 | 29% helix, 22% strand | Q7SID9 |
| B | Cholesterol oxidase (EC 1.1.3.6) | protein | 538 | 30% helix, 22% strand | Q7SID9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.89 | 0.94 | 97 | EDO, FAD |
| 2 | 580 | 0.89 | 0.94 | 81 | EDO, FAD |
| 3 | 274 | 0.62 | 0.80 | 28 | empty |
| 4 | 175 | 0.48 | 0.76 | 23 | empty |
| 5 | 113 | 0.48 | 0.79 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 433 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1I19 · Crystal structure of cholesterol oxidase from B.STEROLICUM · 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 Q7SID9
- Elsewhere: RCSB PDB 1I19 · PDBe 1I19 · UniProt Q7SID9
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