MolNFT v1 · #137659 · protein
Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-amino-4-methylquinolin-7-YL)METHYL)AMINO) ETHYL)BENZONITRILE
5VVD · Nitric oxide synthase, endothelial: “Structure of human endothelial nitric oxide synthase heme domain in complex with…”. X-ray diffraction, 6 ligands (HEM, H4B, 9OG), 18 pockets (best druggability 0.85). MolNFT v1 #137659 on…
- PDB
- 5VVD
- Type
- protein
- Length
- 1,609 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, 9OG, GD, ZN, CL
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 16% strand | P29474 |
| B, D | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 402 | 39% helix, 15% strand | P29474 |
| C | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 401 | 39% helix, 16% 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
- 9OG · 4-(2-{[(2-amino-4-methylquinolin-7-yl) methyl]amino}ethyl)benzonitrile · 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
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.85 | 0.86 | 97 | HEM, H4B, 9OG, CL |
| 2 | 1098 | 0.85 | 0.85 | 92 | HEM, H4B, 9OG, CL |
| 3 | 1052 | 0.84 | 0.85 | 90 | HEM, H4B, 9OG, CL |
| 4 | 1145 | 0.84 | 0.84 | 82 | HEM, H4B, 9OG, CL |
| 5 | 84 | 0.70 | 0.94 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2694 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2678 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VVD · 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 5VVD · PDBe 5VVD · UniProt P29474
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