Research workbench
Crystal structure of the homospermidine synthase (hss) variant W229F from blastochloris viridis in complex with NAD
Analyse Crystal structure of the homospermidine synthase (hss) variant W229F from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S4D
- 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
- 1PS, NAD
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homospermidine synthase (EC 2.5.1.44) | protein | 475 | 36% helix, 25% strand | O32323 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 3 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.80 | 0.81 | 126 | 1PS |
| 2 | 557 | 0.80 | 0.86 | 72 | NAD |
| 3 | 550 | 0.79 | 0.85 | 73 | NAD |
| 4 | 84 | 0.75 | 0.97 | 18 | empty |
| 5 | 124 | 0.66 | 0.89 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1754 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6S4D · Crystal Structure of the Homospermidine Synthase (HSS) variant W229F from Blastochloris… · 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 6S4D · PDBe 6S4D · UniProt O32323
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