Research workbench
Rat neuronal nos heme domain with D-lysine-D-nitroarginine amide bound
Analyse Rat neuronal nos heme domain with D-lysine-D-nitroarginine amide bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RS6
- Type
- protein
- Length
- 817 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
- MTL, HEM, H4B, DP2, ZN
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric-oxide synthase, brain (EC 1.14.13.39) | protein | 407 | 41% helix, 14% strand | P29476 |
| B | Nitric-oxide synthase, brain (EC 1.14.13.39) | protein | 410 | 40% helix, 14% strand | P29476 |
Ligands and binding sites
- MTL · D-mannitol · ligand · 2 copies · chains A, B
- 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
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.84 | 0.84 | 90 | MTL, ACT, HEM, H4B, DP2 |
| 2 | 1130 | 0.84 | 0.84 | 79 | ACT, HEM, H4B, DP2 |
| 3 | 122 | 0.46 | 0.78 | 27 | empty |
| 4 | 125 | 0.44 | 0.77 | 24 | empty |
| 5 | 50 | 0.41 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2740 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 1RS6 · Rat neuronal NOS heme domain with D-lysine-D-nitroarginine amide bound · the same entry in another collection · chain B against B, 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 1RS6 · PDBe 1RS6 · UniProt P29476
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