Research workbench
Covalent adduct between polyamine oxidase and N1ETHYLN11((CYCLOHEPTYL)METHYL)4,8DIAZAUNDECANE at pH 4.6
Analyse Covalent adduct between polyamine oxidase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H84
- Type
- protein
- Length
- 1,383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine oxidase
- EC
- 1.5.3.11
- UniProt
- O64411
- Ligands
- FAD, NBA, NAG, MAN, FCA
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine oxidase (EC 1.5.3.11) | protein | 459 | 33% helix, 22% strand | O64411 |
| B, C | Polyamine oxidase (EC 1.5.3.11) | protein | 462 | 34% helix, 22% strand | O64411 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- NBA · 3-[(3-{[3-(methylamino)propyl]amino}propyl)amino]propane-1,1-diol · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FCA · alpha-D-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.84 | 0.88 | 94 | empty |
| 2 | 709 | 0.83 | 0.87 | 83 | FAD, NBA |
| 3 | 707 | 0.83 | 0.86 | 80 | FAD, NBA |
| 4 | 673 | 0.82 | 0.86 | 74 | FAD, NBA |
| 5 | 70 | 0.61 | 0.91 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1906 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1H84 · COVALENT ADDUCT BETWEEN POLYAMINE OXIDASE AND N1ethylN11((cycloheptyl)methyl)4,8diazaundec… · the same entry in another collection · chain A against A, TM-score 1.00
- O64411 · AlphaFold monomer V2.0 prediction for polyamine oxidase 1 (O64411) · 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 O64411
- Elsewhere: RCSB PDB 1H84 · PDBe 1H84 · UniProt O64411
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