Research workbench
Crystal structure of the homospermidine synthase (hss) variant E117Q from blastochloris viridis in complex with NAD
Analyse Crystal structure of the homospermidine synthase (hss) variant E117Q from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S6G
- Type
- protein
- Length
- 937 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, 1PS, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homospermidine synthase (EC 2.5.1.44) | protein | 469 | 36% helix, 26% strand | O32323 |
| B | Homospermidine synthase (EC 2.5.1.44) | protein | 468 | 37% helix, 25% strand | O32323 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.79 | 0.80 | 80 | empty |
| 2 | 683 | 0.78 | 0.83 | 81 | NAD |
| 3 | 726 | 0.78 | 0.82 | 85 | NAD |
| 4 | 88 | 0.75 | 0.97 | 19 | empty |
| 5 | 111 | 0.64 | 0.89 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1534 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6S6G · Crystal Structure of the Homospermidine Synthase (HSS) variant E117Q 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 6S6G · PDBe 6S6G · UniProt O32323
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