MolNFT v1 · #72974 · protein
Murine inducible nitric oxide synthase oxygenase dimer (delta 65) with tetrahydrobiopterin and product analogue L-thiocitrulline
3NOD: “Murine inducible nitric oxide synthase oxygenase dimer (delta 65) with tetrahydrobiopterin and product…”. X-ray diffraction, 4 ligands (HEM, H4B, SCI), 7 pockets (best druggability 0.82). MolNFT v1 #72974 on GenesisL1: 3D structure…
- PDB
- 3NOD
- Type
- protein
- Length
- 827 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
- P29477
- Ligands
- HEM, H4B, SCI, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase (EC 1.14.13.39) | protein | 414 | 40% helix, 14% strand | P29477 |
| B | Nitric oxide synthase (EC 1.14.13.39) | protein | 413 | 41% helix, 14% strand | P29477 |
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
- SCI · L-thiocitrulline · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.82 | 0.82 | 67 | HEM, H4B, SCI |
| 2 | 1049 | 0.81 | 0.82 | 68 | HEM, H4B, SCI |
| 3 | 284 | 0.61 | 0.79 | 32 | empty |
| 4 | 90 | 0.50 | 0.83 | 20 | empty |
| 5 | 61 | 0.47 | 0.85 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 251 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NOD · Murine inducible nitric oxide synthase oxygenase dimer (delta 65) with… · the same entry in another collection · chain A against A, TM-score 1.00
- P29477 · AlphaFold monomer V2.0 prediction for nitric oxide synthase, inducible (P29477) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P29477
- Elsewhere: RCSB PDB 3NOD · PDBe 3NOD · UniProt P29477
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