MolNFT v1 · #69565 · protein
X-ray structure of the mutant LYS300MET of polyamine oxidase from zea mays in complex with spermine
3KU9: “X-ray structure of the mutant LYS300MET of polyamine oxidase from zea mays in complex with spermine”. X-ray diffraction, 5 ligands (FAD, SPM, NAG), 12 pockets (best druggability 0.86). MolNFT v1 #69565 on GenesisL1: 3D structure…
- PDB
- 3KU9
- Type
- protein
- Length
- 932 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine oxidase
- EC
- 1.5.3.-
- UniProt
- O64411
- Ligands
- FAD, SPM, NAG, CL, SO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine oxidase (EC 1.5.3.-) | protein | 467 | 33% helix, 22% strand | O64411 |
| B | Polyamine oxidase (EC 1.5.3.-) | protein | 465 | 33% helix, 22% strand | O64411 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SPM · Spermine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A
- CL · Chloride ion · ion · chains B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.86 | 0.93 | 67 | empty |
| 2 | 699 | 0.83 | 0.86 | 80 | FAD, SPM |
| 3 | 653 | 0.82 | 0.86 | 80 | FAD, SPM |
| 4 | 91 | 0.73 | 0.95 | 29 | empty |
| 5 | 453 | 0.69 | 0.80 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 1870 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 3KU9 · X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex… · 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 3KU9 · PDBe 3KU9 · UniProt O64411
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