Research workbench
Crystal structure of the homospermidine synthase (hss) from blastochloris viridis in complex with NAD and agmatine
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
- 4XR4
- Type
- protein
- Length
- 948 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
- 1PS, AG2, NAD, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homospermidine synthase (EC 2.5.1.44) | protein | 474 | 35% helix, 24% strand | O32323 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains A, B
- AG2 · Agmatine · ligand · 3 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 8 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.81 | 0.82 | 82 | 1PS |
| 2 | 589 | 0.79 | 0.85 | 82 | NAD, ACT |
| 3 | 516 | 0.79 | 0.86 | 72 | NAD |
| 4 | 85 | 0.74 | 0.97 | 20 | empty |
| 5 | 95 | 0.63 | 0.89 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1650 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4XR4 · Crystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in… · the same entry in another collection · chain B against B, 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 4XR4 · PDBe 4XR4 · UniProt O32323
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