MolNFT v1 · #110256 · protein
Crystal structure of the homospermidine synthase (hss) from blastochloris viridis in complex with NAD and agmatine
4XR4: “Crystal structure of the homospermidine synthase (hss) from blastochloris viridis in complex with NAD and…”. X-ray diffraction, 4 ligands (1PS, AG2, NAD), 8 pockets (best druggability 0.81). MolNFT v1 #110256 on GenesisL1: 3D…
- 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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