MolNFT v1 · #11136 · protein
Crystal structure of hormone receptor
1JDN · Atrial natriuretic peptide clearance receptor: “Crystal structure of hormone receptor”. X-ray diffraction, 6 ligands (BMA, NAG, MAN), 5 pockets (best druggability 0.72). MolNFT v1 #11136 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JDN
- Type
- protein
- Length
- 407 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atrial natriuretic peptide clearance receptor
- UniProt
- P17342
- Ligands
- BMA, NAG, MAN, NDG, FUC, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atrial natriuretic peptide clearance receptor | protein | 407 | 39% helix, 21% strand | P17342 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.98 | 17 | empty |
| 2 | 244 | 0.63 | 0.81 | 32 | NAG, NDG |
| 3 | 232 | 0.57 | 0.79 | 36 | empty |
| 4 | 178 | 0.52 | 0.78 | 24 | empty |
| 5 | 64 | 0.27 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P17342
- Elsewhere: RCSB PDB 1JDN · PDBe 1JDN · UniProt P17342
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