MolNFT v1 · #88716 · protein
Structure of bacillus subtilis nitric oxide synthase in complex with 6,6'-((5-(3-aminopropyl)-1,3-PHENYLENE)BIS( ethane-2,1-DIYL))BIS(4-methylpyridin-2-amine)
4D3K · Nitric oxide synthase oxygenase: “Structure of bacillus subtilis nitric oxide synthase in complex with…”. X-ray diffraction, 3 ligands (HEM, 12S, CL), 10 pockets (best druggability 0.79). MolNFT v1 #88716 on GenesisL1: 3D structure…
- PDB
- 4D3K
- Type
- protein
- Length
- 723 residues
- Chains
- 2
- 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, 12S, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase oxygenase (EC 1.14.13.165) | protein | 362 | 44% helix, 15% strand | O34453 |
| B | Nitric oxide synthase oxygenase (EC 1.14.13.165) | protein | 361 | 45% helix, 15% strand | O34453 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 12S · 6,6'-{[5-(3-aminopropyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine) · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.79 | 0.82 | 64 | HEM, CL, 12S |
| 2 | 820 | 0.79 | 0.82 | 58 | HEM, CL, 12S |
| 3 | 103 | 0.43 | 0.78 | 24 | empty |
| 4 | 65 | 0.39 | 0.80 | 19 | empty |
| 5 | 65 | 0.39 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1404 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4D3K · 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 B 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 4D3K · PDBe 4D3K · UniProt O34453
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