Research workbench
Structure of bovine endothelial nitric oxide synthase heme domain in complex WITH2-(2-(1H-imidazol-1-YL)PYRIMIDIN-4-yl)-N- (3-CYANOBENZYL)ETHAN-1-amine
Analyse Structure of bovine endothelial nitric oxide synthase heme domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D39
- Type
- protein
- Length
- 809 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, endothelial
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, H4B, OLW, MTL, ZN
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 405 | 40% helix, 15% strand | P29473 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 41% helix, 16% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 2 copies · chains A, B
- OLW · 3-[({2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}amino)methyl]benzonitrile · ligand · 2 copies · chains A, B
- MTL · D-mannitol · 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.85 | 0.85 | 108 | HEM, H4B, OLW, ACT, MTL, GOL |
| 2 | 1154 | 0.84 | 0.84 | 94 | HEM, H4B, OLW, ACT, MTL, GOL |
| 3 | 86 | 0.72 | 0.95 | 21 | empty |
| 4 | 98 | 0.56 | 0.85 | 19 | empty |
| 5 | 93 | 0.55 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2913 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4D39 · Structure of bovine endothelial nitric oxide synthase heme domain in complex… · 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 4D39 · PDBe 4D39 · UniProt P29473
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