Research workbench
Crystal structure of truncated catechol oxidase from aspergillus oryzae
Analyse Crystal structure of truncated catechol oxidase from aspergillus oryzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J3Q
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol oxidase
- EC
- 1.10.3.1
- UniProt
- Q2UNF9
- Ligands
- NAG, CU
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catechol oxidase (EC 1.10.3.1) | protein | 338 | 36% helix, 13% strand | Q2UNF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.78 | 0.90 | 53 | empty |
| 2 | 243 | 0.77 | 0.90 | 46 | empty |
| 3 | 909 | 0.70 | 0.75 | 62 | empty |
| 4 | 99 | 0.48 | 0.80 | 20 | empty |
| 5 | 56 | 0.39 | 0.80 | 14 | NAG |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4J3Q · Crystal structure of truncated catechol oxidase from Aspergillus oryzae · 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 4J3Q · PDBe 4J3Q · UniProt Q2UNF9
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