Research workbench
Structure of bacillus subtilis nitric oxide synthase in complex with 3-(2-(6-amino-4-methylpyridin-2-YL)ETHYL)-5-((2-(pyridin-2-YL)ETHYL) AMINO)BENZONITRILE
Analyse Structure of bacillus subtilis nitric oxide synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D3N
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase oxygenase
- EC
- 1.14.13.165
- UniProt
- O34453
- Ligands
- HEM, SK6
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase oxygenase (EC 1.14.13.165) | protein | 362 | 45% helix, 15% strand | O34453 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- SK6 · 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-{[2-(pyridin-2-yl)ethyl]amino}benzonitrile · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- POL · N-propanol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.77 | 0.82 | 47 | HEM, SK6, GOL, POL |
| 2 | 74 | 0.35 | 0.76 | 15 | empty |
| 3 | 74 | 0.32 | 0.74 | 21 | empty |
Compared structures
- 4D3N · Structure of Bacillus subtilis Nitric Oxide Synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O34453 · AlphaFold monomer V2.0 prediction for nitric oxide synthase oxygenase (O34453) · 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 O34453
- Elsewhere: RCSB PDB 4D3N · PDBe 4D3N · UniProt O34453
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