Research workbench
Structure of bovine endothelial nitric oxide synthase heme domain in complex with (1R,2R)-2-(3-fluorobenzyl)-N-{2-[2- (1H-imidazol-1-YL)PYRIMIDIN-4-YL]ETHYL}CYCLOPROPANAMINE
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
- 4D38
- Type
- protein
- Length
- 807 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, L5Z, ZN
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 41% helix, 16% strand | P29473 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 403 | 40% helix, 15% 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
- L5Z · (1R,2R)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine · 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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.85 | 0.86 | 84 | HEM, H4B, L5Z, ACT, GOL |
| 2 | 1176 | 0.84 | 0.84 | 92 | HEM, H4B, L5Z, ACT, GOL |
| 3 | 86 | 0.71 | 0.95 | 20 | empty |
| 4 | 96 | 0.54 | 0.84 | 20 | empty |
| 5 | 97 | 0.54 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2882 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 4D38 · Structure of bovine endothelial nitric oxide synthase heme domain in complex 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 4D38 · PDBe 4D38 · UniProt P29473
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