MolNFT v1 · #163484 · protein
Crystal structure of the homospermidine synthase (hss) variant W229F from blastochloris viridis in complex with NAD
6S4D: “Crystal structure of the homospermidine synthase (hss) variant W229F from blastochloris viridis in complex…”. X-ray diffraction, 2 ligands (1PS, NAD), 9 pockets (best druggability 0.80). MolNFT v1 #163484 on GenesisL1: 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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