MolNFT v1 · #125683 · protein
Crystal structure of murine N1-acetylpolyamine oxidase in complex with MDL72527
5LGB · Peroxisomal N(1)-acetyl-SPERMINE/SPERMIDINE oxidase…: “Crystal structure of murine N1-acetylpolyamine oxidase in complex with MDL72527”. X-ray diffraction, 2 ligands (6YU, MD2), 5 pockets (best druggability 0.81). MolNFT v1 #125683…
- PDB
- 5LGB
- Type
- protein
- Length
- 456 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal N(1)-acetyl-SPERMINE/SPERMIDINE oxidase, peroxisomal…
- EC
- 1.5.3.13
- UniProt
- Q8C0L6
- Ligands
- 6YU, MD2
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal N(1)-acetyl-SPERMINE/SPERMIDINE oxidase, peroxisomal N(1)-acetyl-SPERMINE/SPERMIDINE oxidase (EC 1.5.3.13) | protein | 456 | 39% helix, 20% strand | Q8C0L6 |
Ligands and binding sites
- 6YU · FAD-MDL72527 adduct · ligand · chains A
- MD2 · N,N'-bis(2,3-butadienyl)-1,4-butane-diamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.81 | 0.84 | 86 | 6YU, MD2 |
| 2 | 100 | 0.34 | 0.73 | 20 | empty |
| 3 | 62 | 0.33 | 0.76 | 16 | empty |
| 4 | 53 | 0.33 | 0.78 | 14 | empty |
| 5 | 59 | 0.30 | 0.75 | 20 | empty |
Compared structures
- 5LGB · Crystal structure of murine N1-acetylpolyamine oxidase in complex with MDL72527 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8C0L6 · AlphaFold monomer V2.0 prediction for peroxisomal N(1)-acetyl- SPERMINE/SPERMIDINE… · 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 Q8C0L6
- Elsewhere: RCSB PDB 5LGB · PDBe 5LGB · UniProt Q8C0L6
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