MolNFT v1 · #88695 · protein
Structure of rat neuronal nitric oxide synthase heme domain in complex with (1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol- 1-YL)PYRIMIDIN-4-YL]ETHYL} cyclopropanamine
4D2Z · Nitric oxide synthase, brain: “Structure of rat neuronal nitric oxide synthase heme domain in complex with…”. X-ray diffraction, 4 ligands (HEM, H4B, K9L), 12 pockets (best druggability 0.84). MolNFT v1 #88695 on GenesisL1: 3D…
- PDB
- 4D2Z
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, brain
- EC
- 1.14.13.39
- UniProt
- P29476
- Ligands
- HEM, H4B, K9L, ZN
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, brain (EC 1.14.13.39) | protein | 407 | 42% helix, 15% strand | P29476 |
| B | Nitric oxide synthase, brain (EC 1.14.13.39) | protein | 411 | 41% helix, 15% strand | P29476 |
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
- K9L · (1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- ACT · Acetate ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.84 | 0.84 | 89 | HEM, H4B, K9L, ACT |
| 2 | 1141 | 0.83 | 0.84 | 91 | HEM, H4B, K9L, ACT |
| 3 | 52 | 0.68 | 0.97 | 22 | empty |
| 4 | 95 | 0.38 | 0.76 | 15 | empty |
| 5 | 53 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2711 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 4D2Z · Structure of rat neuronal nitric oxide synthase heme domain in complex with… · 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 P29476
- Elsewhere: RCSB PDB 4D2Z · PDBe 4D2Z · UniProt P29476
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