MolNFT v1 · #27637 · protein
Crystal structure of FMS1, a polyamine oxidase from yeast
1XPQ · Polyamine oxidase FMS1: “Crystal structure of FMS1, a polyamine oxidase from yeast”. X-ray diffraction, 2 ligands (SPM, FAD), 19 pockets (best druggability 0.88). MolNFT v1 #27637 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1XPQ
- Type
- protein
- Length
- 1,991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine oxidase FMS1
- EC
- 1.5.3.17
- UniProt
- P50264
- Ligands
- SPM, FAD
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine oxidase FMS1 (EC 1.5.3.17) | protein | 502 | 36% helix, 19% strand | P50264 |
| B | Polyamine oxidase FMS1 (EC 1.5.3.17) | protein | 496 | 36% helix, 20% strand | P50264 |
| C | Polyamine oxidase FMS1 (EC 1.5.3.17) | protein | 499 | 35% helix, 21% strand | P50264 |
| D | Polyamine oxidase FMS1 (EC 1.5.3.17) | protein | 494 | 35% helix, 20% strand | P50264 |
Ligands and binding sites
- SPM · Spermine · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.88 | 0.94 | 86 | SPM, FAD |
| 2 | 432 | 0.87 | 0.94 | 80 | SPM, FAD |
| 3 | 442 | 0.86 | 0.94 | 79 | SPM, FAD |
| 4 | 434 | 0.86 | 0.94 | 78 | SPM, FAD |
| 5 | 254 | 0.53 | 0.76 | 34 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1612 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1566 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P50264
- Elsewhere: RCSB PDB 1XPQ · PDBe 1XPQ · UniProt P50264
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