Research workbench
Crystal structure of aspergillus oryzae catechol oxidase in deoxy-form
Analyse Crystal structure of aspergillus oryzae catechol oxidase in deoxy-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OR4
- Type
- protein
- Length
- 1,483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol oxidase
- UniProt
- Q2UNF9
- Ligands
- NAG, BMA, MAN, CU
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Catechol oxidase | protein | 371 | 40% helix, 11% strand | Q2UNF9 |
| C | Catechol oxidase | protein | 370 | 41% helix, 10% strand | Q2UNF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains D, C, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B, D
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.80 | 0.87 | 66 | empty |
| 2 | 344 | 0.79 | 0.89 | 53 | empty |
| 3 | 334 | 0.79 | 0.89 | 56 | empty |
| 4 | 322 | 0.78 | 0.89 | 56 | empty |
| 5 | 262 | 0.68 | 0.84 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–D · 897 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 854 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 829 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 11 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 5OR4 · Crystal structure of Aspergillus oryzae catechol oxidase in deoxy-form · 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 Q2UNF9
- Elsewhere: RCSB PDB 5OR4 · PDBe 5OR4 · UniProt Q2UNF9
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