Research workbench
Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-amino-4-methylquinolin-7-YL)METHYL)AMINO) ethyl)-2-methylbenzonitrile
Analyse Structure of human 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
- 5VVC
- Type
- protein
- Length
- 1,614 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, endothelial
- EC
- 1.14.13.39
- UniProt
- P29474
- Ligands
- HEM, H4B, 9OJ, GD, ZN, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 38% helix, 15% strand | P29474 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 39% helix, 15% strand | P29474 |
| C | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 401 | 40% helix, 15% strand | P29474 |
| D | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 405 | 41% helix, 15% strand | P29474 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 4 copies · chains A, B, C, D
- 9OJ · 4-(2-{[(2-amino-4-methylquinolin-7-yl) methyl]amino}ethyl)-2-methylbenzonitrile · ligand · 4 copies · chains A, B, C, D
- GD · Gadolinium atom · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.86 | 0.86 | 91 | HEM, H4B, 9OJ, CL |
| 2 | 1033 | 0.85 | 0.86 | 84 | HEM, H4B, 9OJ, CL |
| 3 | 1154 | 0.84 | 0.85 | 89 | HEM, H4B, 9OJ, CL |
| 4 | 1194 | 0.83 | 0.84 | 87 | HEM, H4B, 9OJ, CL |
| 5 | 86 | 0.73 | 0.95 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2738 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2720 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 539 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VVC · Structure of human 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 P29474
- Elsewhere: RCSB PDB 5VVC · PDBe 5VVC · UniProt P29474
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