MolNFT v1 · #20857 · protein
Bovine endothelial nos heme domain with D-lysine-D-nitroarginine amide bound
1RS8 · Nitric-oxide synthase, endothelial: “Bovine endothelial nos heme domain with D-lysine-D-nitroarginine amide bound”. X-ray diffraction, 4 ligands (HEM, H4B, DP2), 11 pockets (best druggability 0.86). MolNFT v1 #20857 on GenesisL1: 3D…
- PDB
- 1RS8
- Type
- protein
- Length
- 810 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
- P29473
- Ligands
- HEM, H4B, DP2, ZN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric-oxide synthase, endothelial (EC 1.14.13.39) | protein | 406 | 41% helix, 15% strand | P29473 |
| B | Nitric-oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 16% strand | P29473 |
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
- DP2 · L-lysyl-N~5~-[(Z)-(2,2-dihydroxyhydrazino)(imino)methyl]-L-ornithinamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- ACT · Acetate 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.86 | 0.87 | 108 | ACT, HEM, H4B, DP2, GOL |
| 2 | 1106 | 0.83 | 0.84 | 80 | ACT, HEM, H4B, DP2, GOL |
| 3 | 94 | 0.55 | 0.84 | 20 | empty |
| 4 | 86 | 0.54 | 0.85 | 18 | empty |
| 5 | 115 | 0.46 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2911 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1RS8 · Bovine endothelial NOS heme domain with D-lysine-D-nitroarginine amide bound · the same entry in another collection · chain B against B, TM-score 1.00
- P29473 · AlphaFold monomer V2.0 prediction for nitric oxide synthase, endothelial (P29473) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 1RS8 · PDBe 1RS8 · UniProt P29473
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