MolNFT v1 · #11138 · protein
Crystal structure of HORMONE/RECEPTOR complex
1JDP · Atrial natriuretic peptide clearance receptor: “Crystal structure of HORMONE/RECEPTOR complex”. X-ray diffraction, 2 ligands (NAG, CL), 10 pockets (best druggability 0.69). MolNFT v1 #11138 on GenesisL1: 3D structure, binding sites…
- PDB
- 1JDP
- Type
- protein
- Length
- 809 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Atrial natriuretic peptide clearance receptor; C-type natriuretic peptide
- UniProt
- P17342, P23582
- Ligands
- NAG, CL
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Atrial natriuretic peptide clearance receptor | protein | 396 | 39% helix, 22% strand | P17342 |
| B | Atrial natriuretic peptide clearance receptor | protein | 395 | 39% helix, 23% strand | P17342 |
| H | C-type natriuretic peptide | protein | 18 | 0% helix, 0% strand | P23582 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.69 | 0.78 | 56 | empty |
| 2 | 311 | 0.67 | 0.81 | 30 | empty |
| 3 | 134 | 0.58 | 0.84 | 40 | empty |
| 4 | 163 | 0.54 | 0.80 | 23 | empty |
| 5 | 107 | 0.52 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–H · 775 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 699 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 618 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1JDP · Crystal Structure of Hormone/Receptor Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P17342 · AlphaFold monomer V2.0 prediction for atrial natriuretic peptide receptor 3 (P17342) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P23582 · AlphaFold monomer V2.0 prediction for C-type natriuretic peptide (P23582) · a predicted model of the same protein · chain H against A, TM-score 0.21
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
- Every structure of UniProt P23582
- Elsewhere: RCSB PDB 1JDP · PDBe 1JDP · UniProt P17342 · UniProt P23582
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