MolNFT v1 · #176034 · protein
Spdh spermidine dehydrogenase Y443A mutant
7D9J · Spermidine dehydrogenase, spdh: “Spdh spermidine dehydrogenase Y443A mutant”. X-ray diffraction, 2 ligands (FAD, HEM), 7 pockets (best druggability 0.86). MolNFT v1 #176034 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7D9J
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine dehydrogenase, spdh
- EC
- 1.5.99.6
- UniProt
- Q9HXS8
- Ligands
- FAD, HEM
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine dehydrogenase, spdh (EC 1.5.99.6) | protein | 577 | 37% helix, 21% strand | Q9HXS8 |
| B | Spermidine dehydrogenase, spdh (EC 1.5.99.6) | protein | 587 | 37% helix, 20% strand | Q9HXS8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.86 | 0.87 | 116 | FAD, HEM, GOL |
| 2 | 1092 | 0.85 | 0.86 | 129 | FAD, HEM |
| 3 | 169 | 0.41 | 0.73 | 25 | empty |
| 4 | 97 | 0.39 | 0.76 | 22 | empty |
| 5 | 74 | 0.35 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7D9J · SpdH Spermidine dehydrogenase Y443A mutant · the same entry in another collection · 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 Q9HXS8
- Elsewhere: RCSB PDB 7D9J · PDBe 7D9J · UniProt Q9HXS8
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