Research workbench
Catechol oxidase from ipomoea batatas (sweet potatoes) in the native CU(II)-CU(II) state
Analyse Catechol oxidase from ipomoea batatas (sweet potatoes) in the native… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BT1
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (catechol oxidase)
- EC
- 1.10.3.1
- UniProt
- Q9ZP19
- Ligands
- C2O
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (catechol oxidase) (EC 1.10.3.1) | protein | 336 | 38% helix, 7% strand | Q9ZP19 |
Ligands and binding sites
- C2O · Cu-O-Cu linkage · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.53 | 0.76 | 20 | empty |
| 2 | 78 | 0.41 | 0.79 | 20 | empty |
| 3 | 66 | 0.35 | 0.77 | 20 | empty |
| 4 | 64 | 0.30 | 0.75 | 12 | empty |
| 5 | 66 | 0.29 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 349 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1BT1 · Catechol oxidase from ipomoea batatas (sweet potatoes) in the native CU(II)-CU(II) state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZP19 · AlphaFold monomer V2.0 prediction for polyphenol oxidase I, chloroplastic (Q9ZP19) · a predicted model of the same protein · 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 Q9ZP19
- Elsewhere: RCSB PDB 1BT1 · PDBe 1BT1 · UniProt Q9ZP19
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