MolNFT v1 · #72347 · protein
Structure of endothelial nitric oxide synthase heme domain complexed with 6,6'-(2,2'-(pyridine-3,5-DIYL)BIS(ETHANE-2,1-DIYL))BIS(4- methylpyridin-2-amine)
3N5T: “Structure of endothelial nitric oxide synthase heme domain complexed with…”. X-ray diffraction, 5 ligands (HEM, XFJ, H4B), 10 pockets (best druggability 0.85). MolNFT v1 #72347 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3N5T
- Type
- protein
- Length
- 808 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, XFJ, H4B, CAD, ZN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase (EC 1.14.13.39) | protein | 405 | 41% helix, 15% strand | P29473 |
| B | Nitric oxide synthase (EC 1.14.13.39) | protein | 403 | 38% helix, 17% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- XFJ · 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine) · ligand · 2 copies · chains A, B
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 2 copies · chains A, B
- CAD · Cacodylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.85 | 0.86 | 95 | HEM, ACT, GOL, XFJ, H4B |
| 2 | 912 | 0.83 | 0.85 | 81 | HEM, ACT, GOL, XFJ, H4B |
| 3 | 100 | 0.56 | 0.85 | 20 | empty |
| 4 | 92 | 0.53 | 0.84 | 19 | empty |
| 5 | 161 | 0.48 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2849 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3N5T · Structure of endothelial nitric oxide synthase heme domain complexed with… · the same entry in another collection · 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 P29473
- Elsewhere: RCSB PDB 3N5T · PDBe 3N5T · UniProt P29473
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