MolNFT v1 · #176032 · protein
Spdh spermidine dehydrogenase N33 truncation structure
7D9H · Spermidine dehydrogenase, spdh: “Spdh spermidine dehydrogenase N33 truncation structure”. X-ray diffraction, 2 ligands (FAD, HEM), 8 pockets (best druggability 0.86). MolNFT v1 #176032 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D9H
- Type
- protein
- Length
- 1,159 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
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine dehydrogenase, spdh (EC 1.5.99.6) | protein | 572 | 36% 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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.86 | 0.87 | 125 | FAD, HEM, GOL |
| 2 | 1038 | 0.84 | 0.85 | 109 | FAD, HEM, GOL |
| 3 | 171 | 0.47 | 0.76 | 29 | empty |
| 4 | 84 | 0.38 | 0.77 | 28 | empty |
| 5 | 84 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7D9H · SpdH Spermidine dehydrogenase N33 truncation structure · 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 7D9H · PDBe 7D9H · UniProt Q9HXS8
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