Research workbench
Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2A resolution
Analyse Crystal structure of a eukaryotic (pea seedling) copper-containing amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KSI
- Type
- protein
- Length
- 1,284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- Q43077
- Ligands
- NAG, CU, MN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Copper amine oxidase (EC 1.4.3.6) | protein | 642 | 13% helix, 43% strand | Q43077 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.87 | 0.92 | 97 | empty |
| 2 | 533 | 0.84 | 0.90 | 87 | empty |
| 3 | 129 | 0.79 | 0.97 | 35 | empty |
| 4 | 123 | 0.79 | 0.97 | 32 | empty |
| 5 | 422 | 0.73 | 0.83 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 7887 Ų buried · 153 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 1KSI · Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2A… · the same entry in another collection · chain A against A, TM-score 1.00
- Q43077 · AlphaFold monomer V2.0 prediction for primary amine oxidase (Q43077) · 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 Q43077
- Elsewhere: RCSB PDB 1KSI · PDBe 1KSI · UniProt Q43077
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