MolNFT v1 · #88659 · protein
Structure of human endothelial nitric oxide synthase heme domain in complex with 6-((((3S, 5R)-5-(((6-amino-4- methylpyridin-2-YL)METHOXY)METHYL)PYRROLIDIN-3-YL)OXY) methyl)-4-methylpyridin-2-amine
4D1P · Nitric oxide synthase, endothelial: “Structure of human endothelial nitric oxide synthase heme domain in complex with 6-((((3S…”. X-ray diffraction, 5 ligands (HEM, H4B, Q16), 10 pockets (best druggability 0.85). MolNFT v1 #88659 on…
- PDB
- 4D1P
- Type
- protein
- Length
- 803 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
- P29474
- Ligands
- HEM, H4B, Q16, GD, ZN
- Pockets
- 10 · 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 | 401 | 40% helix, 16% strand | P29474 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 402 | 41% helix, 16% strand | P29474 |
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
- Q16 · 6-((((3S, 5R)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine · ligand · 2 copies · chains A, B
- GD · Gadolinium atom · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains B, A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.85 | 0.86 | 81 | ACT, HEM, H4B, Q16 |
| 2 | 1069 | 0.85 | 0.85 | 86 | HEM, H4B, Q16, ACT |
| 3 | 85 | 0.70 | 0.94 | 22 | empty |
| 4 | 89 | 0.56 | 0.86 | 18 | empty |
| 5 | 94 | 0.54 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2743 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4D1P · 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 4D1P · PDBe 4D1P · UniProt P29474
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