MolNFT v2 · #1571 · protein
A 30 ångström U-shaped catalytic tunnel in the crystal structure of polyamine oxidase
1B5Q · Protein (polyamine oxidase): “A 30 ångström U-shaped catalytic tunnel in the crystal structure of polyamine oxidase”. X-ray diffraction at 1.9, 5 ligands (FAD, MD2, NAG), 15 pockets (best druggability 0.84). MolNFT v2 #1571 on…
- PDB
- 1B5Q
- Type
- protein
- Length
- 1,383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Zea mays
- Molecule
- Protein (polyamine oxidase)
- Ligands
- FAD, MD2, NAG, MAN, FCA
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (polyamine oxidase) | protein | 459 | 33% helix, 22% strand | — |
| B, C | Protein (polyamine oxidase) | protein | 462 | 34% helix, 22% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- MD2 · N,N'-bis(2,3-butadienyl)-1,4-butane-diamine · 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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.84 | 0.85 | 108 | FAD, MD2 |
| 2 | 777 | 0.84 | 0.87 | 95 | empty |
| 3 | 807 | 0.84 | 0.86 | 100 | FAD, MD2 |
| 4 | 756 | 0.83 | 0.86 | 83 | FAD, MD2 |
| 5 | 152 | 0.56 | 0.82 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1903 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1B5Q · A 30 ångström U-shaped catalytic tunnel in the crystal structure of polyamine oxidase · 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
- Elsewhere: RCSB PDB 1B5Q · PDBe 1B5Q
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