Research workbench
Hansenula polymorpha copper amine oxidase-1 in complex with CU(I)
Analyse Hansenula polymorpha copper amine oxidase-1 in complex with CU(I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T0U
- Type
- protein
- Length
- 1,990 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal primary amine oxidase
- EC
- 1.4.3.21
- UniProt
- P12807
- Ligands
- CU1, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 657 | 16% helix, 40% strand | P12807 |
| B | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 668 | 16% helix, 39% strand | P12807 |
| C | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 665 | 16% helix, 38% strand | P12807 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 19 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.82 | 0.92 | 73 | GOL |
| 2 | 225 | 0.80 | 0.94 | 32 | empty |
| 3 | 217 | 0.78 | 0.92 | 33 | empty |
| 4 | 829 | 0.77 | 0.81 | 128 | empty |
| 5 | 207 | 0.73 | 0.88 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 7514 Ų buried · 144 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 248 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3T0U · Hansenula polymorpha copper amine oxidase-1 in complex with Cu(I) · the same entry in another collection · chain A against A, TM-score 1.00
- P12807 · AlphaFold monomer V2.0 prediction for peroxisomal primary amine oxidase (P12807) · 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 P12807
- Elsewhere: RCSB PDB 3T0U · PDBe 3T0U · UniProt P12807
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