MolNFT v1 · #4391 · protein
Bovine endothelial nitric oxide synthase heme domain complexed with 6S-H4B
1DMI: “Bovine endothelial nitric oxide synthase heme domain complexed with 6S-H4B”. X-ray diffraction, 4 ligands (HEM, BHS, ITU), 12 pockets (best druggability 0.86). MolNFT v1 #4391 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1DMI
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase
- EC
- 1.14.13.39
- UniProt
- P29473
- Ligands
- HEM, BHS, ITU, ZN
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase (EC 1.14.13.39) | protein | 416 | 38% helix, 15% strand | P29473 |
| B | Nitric oxide synthase (EC 1.14.13.39) | protein | 414 | 39% helix, 16% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- BHS · 6S-5,6,7,8-tetrahydrobiopterin · ligand · 2 copies · chains A, B
- ITU · Ethylisothiourea · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- CAC · Cacodylate 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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.86 | 0.86 | 102 | ACT, HEM, BHS, ITU, GOL |
| 2 | 1157 | 0.84 | 0.85 | 95 | ACT, HEM, BHS, ITU, GOL |
| 3 | 89 | 0.72 | 0.95 | 22 | empty |
| 4 | 295 | 0.57 | 0.77 | 40 | empty |
| 5 | 251 | 0.56 | 0.78 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2901 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1DMI · Bovine endothelial nitric oxide synthase heme domain complexed with 6S-H4B · 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 1DMI · PDBe 1DMI · UniProt P29473
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