MolNFT v1 · #69402 · protein
X-ray structure of the mutant LYS300MET of polyamine oxidase from zea mays
3KPF: “X-ray structure of the mutant LYS300MET of polyamine oxidase from zea mays”. X-ray diffraction, 4 ligands (FAD, NAG, CL), 14 pockets (best druggability 0.86). MolNFT v1 #69402 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3KPF
- Type
- protein
- Length
- 931 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, NAG, CL, SO4
- Pockets
- 14 · 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 | 34% helix, 22% strand | O64411 |
| B | Polyamine oxidase (EC 1.5.3.-) | protein | 464 | 32% helix, 21% strand | O64411 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · 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 A
- SO4 · Sulfate ion · ion · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.86 | 0.94 | 64 | empty |
| 2 | 724 | 0.84 | 0.87 | 86 | FAD |
| 3 | 699 | 0.84 | 0.87 | 87 | FAD |
| 4 | 304 | 0.56 | 0.76 | 27 | empty |
| 5 | 231 | 0.56 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1863 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 3KPF · X-ray structure of the mutant Lys300Met of polyamine oxidase from Zea mays · 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 3KPF · PDBe 3KPF · UniProt O64411
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