MolNFT v1 · #4380 · protein
Bovine endothelial nitric oxide synthase heme domain complexed with homoarginine (H4B free)
1DM7: “Bovine endothelial nitric oxide synthase heme domain complexed with homoarginine (H4B free)”. X-ray diffraction, 3 ligands (HEM, HRG, ZN), 11 pockets (best druggability 0.86). MolNFT v1 #4380 on GenesisL1: 3D structure, binding…
- PDB
- 1DM7
- 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, HRG, ZN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% 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 | 37% helix, 17% strand | P29473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- HRG · L-homoarginine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- CAC · Cacodylate ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.86 | 93 | GOL, ACT, HEM, HRG |
| 2 | 1152 | 0.85 | 0.85 | 98 | ACT, HEM, HRG, GOL |
| 3 | 94 | 0.72 | 0.95 | 21 | empty |
| 4 | 299 | 0.62 | 0.79 | 49 | empty |
| 5 | 92 | 0.55 | 0.85 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2883 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 1DM7 · Bovine endothelial nitric oxide synthase heme domain complexed with homoarginine (H4B… · 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 1DM7 · PDBe 1DM7 · UniProt P29473
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