MolNFT v1 · #59103 · protein
Crystal structure of polyamine oxidase FMS1 from saccharomyces cerevisiae in complex with bis-(3S,3'S)- methylated spermine
3BNU: “Crystal structure of polyamine oxidase FMS1 from saccharomyces cerevisiae in complex with bis-(3S,3'S)…”. X-ray diffraction, 2 ligands (FAD, SPZ), 9 pockets (best druggability 0.87). MolNFT v1 #59103 on GenesisL1: 3D structure…
- PDB
- 3BNU
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine oxidase FMS1
- EC
- 1.5.3.11
- UniProt
- P50264
- Ligands
- FAD, SPZ
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Polyamine oxidase FMS1 (EC 1.5.3.11) | protein | 499 | 37% helix, 19% strand | P50264 |
| A | Polyamine oxidase FMS1 (EC 1.5.3.11) | protein | 497 | 37% helix, 21% strand | P50264 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, A
- SPZ · (3S,3'S)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.87 | 0.92 | 92 | FAD, SPZ |
| 2 | 547 | 0.87 | 0.92 | 84 | FAD, SPZ |
| 3 | 168 | 0.47 | 0.76 | 28 | empty |
| 4 | 161 | 0.45 | 0.75 | 25 | empty |
| 5 | 172 | 0.44 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- B–A · 1551 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BNU · Crystal structure of polyamine oxidase FMS1 from Saccharomyces cerevisiae in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P50264 · AlphaFold monomer V2.0 prediction for polyamine oxidase FMS1 (P50264) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3BNU · PDBe 3BNU · UniProt P50264
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