MolNFT v1 · #3747 · protein
Bovine endothelial nitric oxide synthase heme domain complexed with 1, 3-pbitu (H4B free)
1D1Y: “Bovine endothelial nitric oxide synthase heme domain complexed with 1, 3-pbitu (H4B free)”. X-ray diffraction, 4 ligands (HEM, 3BT, CAD), 14 pockets (best druggability 0.86). MolNFT v1 #3747 on GenesisL1: 3D structure, binding sites…
- PDB
- 1D1Y
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bovine endothelial nitric oxide synthase heme domain
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, 3BT, CAD, ZN
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bovine endothelial nitric oxide synthase heme domain (EC 1.14.13.39) | protein | 416 | 38% helix, 15% strand | P29473 |
| B | Bovine endothelial nitric oxide synthase heme domain (EC 1.14.13.39) | protein | 414 | 38% helix, 14% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 3BT · 2-{2-[3-(2-carbamimidoylsulfanyl-ethyl)-phenyl]-ethyl}-isothiourea · ligand · 2 copies · chains A, B
- CAD · Cacodylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.86 | 0.87 | 91 | ACT, HEM, 3BT, EDO, GOL |
| 2 | 1114 | 0.85 | 0.86 | 95 | GOL, ACT, HEM, 3BT, EDO |
| 3 | 98 | 0.73 | 0.95 | 22 | empty |
| 4 | 366 | 0.64 | 0.79 | 61 | empty |
| 5 | 96 | 0.54 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2900 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 1D1Y · Bovine endothelial nitric oxide synthase heme domain complexed with 1,3-pbitu (H4B free) · 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 1D1Y · PDBe 1D1Y · UniProt P29473
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