Research workbench
Crystal structure of the homospermidine synthase (hss) variant W229A from blastochloris viridis in complex with NAD and put
Analyse Crystal structure of the homospermidine synthase (hss) variant W229A from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S72
- 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, PUT
- Pockets
- 12 · best druggability 0.81
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
- PUT · 1,4-diaminobutane · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.81 | 0.87 | 71 | NAD |
| 2 | 585 | 0.81 | 0.86 | 73 | NAD, PUT |
| 3 | 84 | 0.76 | 0.97 | 19 | empty |
| 4 | 791 | 0.75 | 0.80 | 79 | empty |
| 5 | 326 | 0.70 | 0.83 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1759 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6S72 · Crystal Structure of the Homospermidine Synthase (HSS) variant W229A 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 6S72 · PDBe 6S72 · UniProt O32323
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