Research workbench
Crystal structure of the homospermidine synthase (hss) from blastochloris viridis in complex with NAD and 1,3-diaminopropane.
Analyse Crystal structure of the homospermidine synthase (hss) from blastochloris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQC
- Type
- protein
- Length
- 950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homospermidine synthase
- EC
- 2.5.1.44
- UniProt
- O32323
- Ligands
- NAD, 13D, 1PS
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homospermidine synthase (EC 2.5.1.44) | protein | 475 | 36% helix, 24% strand | O32323 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 13D · 1,3-diaminopropane · ligand · 2 copies · chains A
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.79 | 0.87 | 74 | NAD, 13D |
| 2 | 499 | 0.78 | 0.85 | 70 | NAD |
| 3 | 83 | 0.75 | 0.98 | 18 | empty |
| 4 | 426 | 0.74 | 0.84 | 58 | 1PS, ACT |
| 5 | 655 | 0.73 | 0.80 | 74 | 13D, 1PS, ACT |
Interfaces
1 interface between chains.
- A–B · 1777 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4XQC · Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in… · the same entry in another collection · chain A against A, TM-score 1.00
- O32323 · AlphaFold monomer V2.0 prediction for homospermidine synthase (O32323) · 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 O32323
- Elsewhere: RCSB PDB 4XQC · PDBe 4XQC · UniProt O32323
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