MolNFT v1 · #113478 · protein
Structure of rat neuronal nitric oxide synthase heme domain in complex with (S)-2-amino-5-(2-mercaptoacetimidamido) pentanoic acid
5AGO · Nitric oxide synthase, brain: “Structure of rat neuronal nitric oxide synthase heme domain in complex with…”. X-ray diffraction, 4 ligands (HEM, H4B, VUR), 11 pockets (best druggability 0.86). MolNFT v1 #113478 on GenesisL1: 3D…
- PDB
- 5AGO
- 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, VUR, ZN
- Pockets
- 11 · best druggability 0.86
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, 14% strand | P29476 |
| B | Nitric oxide synthase, brain (EC 1.14.13.39) | protein | 411 | 40% 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
- VUR · (S)-2-amino-5-(2-mercaptoacetimidamido)pentanoic acid · 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
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 | 658 | 0.86 | 0.90 | 105 | HEM, H4B, VUR |
| 2 | 273 | 0.77 | 0.89 | 40 | HEM, VUR |
| 3 | 81 | 0.62 | 0.90 | 16 | H4B |
| 4 | 241 | 0.53 | 0.76 | 39 | empty |
| 5 | 120 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2753 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5AGO · 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
- P29476 · AlphaFold monomer V2.0 prediction for nitric oxide synthase, brain (P29476) · 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 P29476
- Elsewhere: RCSB PDB 5AGO · PDBe 5AGO · UniProt P29476
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