Research workbench
Crystal structure of multi-copper oxidase from pediococcus acidilactici
Analyse Crystal structure of multi-copper oxidase from pediococcus acidilactici in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XIZ
- Type
- protein
- Length
- 949 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper oxidase
- UniProt
- A0A1A5VCP7
- Ligands
- C2O, BEN, CU, CL
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper oxidase | protein | 477 | 7% helix, 41% strand | A0A1A5VCP7 |
| B | Copper oxidase | protein | 472 | 7% helix, 42% strand | A0A1A5VCP7 |
Ligands and binding sites
- C2O · Cu-O-Cu linkage · ligand · 2 copies · chains A, B
- BEN · Benzamidine · ligand · chains A, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.75 | 0.82 | 83 | CL, BEN |
| 2 | 317 | 0.59 | 0.77 | 42 | CL |
| 3 | 156 | 0.53 | 0.80 | 23 | empty |
| 4 | 91 | 0.49 | 0.82 | 30 | empty |
| 5 | 97 | 0.45 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6XIZ · Crystal structure of multi-copper oxidase from Pediococcus acidilactici · 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 A0A1A5VCP7
- Elsewhere: RCSB PDB 6XIZ · PDBe 6XIZ · UniProt A0A1A5VCP7
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