Research workbench
Hansenula polymorpha copper amine oxidase-1 in complex with CO(II)
Analyse Hansenula polymorpha copper amine oxidase-1 in complex with CO(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SXX
- Type
- protein
- Length
- 3,974 residues
- Chains
- 6
- 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
- CO, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 666 | 15% helix, 39% strand | P12807 |
| B | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 664 | 15% helix, 39% strand | P12807 |
| C | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 666 | 15% helix, 39% strand | P12807 |
| D | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 657 | 16% helix, 39% strand | P12807 |
| E | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 656 | 15% helix, 39% strand | P12807 |
| F | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 665 | 15% helix, 39% strand | P12807 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains C, F
- GOL · Glycerol · additive · 43 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.88 | 0.91 | 121 | GOL |
| 2 | 551 | 0.87 | 0.93 | 104 | GOL |
| 3 | 349 | 0.82 | 0.91 | 55 | empty |
| 4 | 254 | 0.81 | 0.93 | 46 | empty |
| 5 | 253 | 0.81 | 0.93 | 46 | empty |
Interfaces
12 interfaces between chains.
- A–B · 7736 Ų buried · 152 hydrogen bonds · protein-protein
- E–F · 7430 Ų buried · 143 hydrogen bonds · protein-protein
- C–D · 7402 Ų buried · 141 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 538 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3SXX · Hansenula polymorpha copper amine oxidase-1 in complex with Co(II) · the same entry in another collection · chain F against F, TM-score 1.00
- P12807 · AlphaFold monomer V2.0 prediction for peroxisomal primary amine oxidase (P12807) · a predicted model of the same protein · chain E 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 3SXX · PDBe 3SXX · UniProt P12807
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