MolNFT v1 · #176152 · protein
Structure of calcium-sensing receptor in complex with nps-2143
7DD5: “Structure of calcium-sensing receptor in complex with nps-2143”. Electron microscopy, 5 ligands (TRP, YP1, NAG), 20 pockets (best druggability 0.89). MolNFT v1 #176152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DD5
- Type
- protein
- Length
- 1,597 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-sensing receptor
- Ligands
- TRP, YP1, NAG, CA, CL
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-sensing receptor | protein | 798 | 43% helix, 15% strand | — |
| B | Calcium-sensing receptor | protein | 799 | 42% helix, 15% strand | — |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- YP1 · 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.89 | 0.91 | 139 | CA, TRP, CL |
| 2 | 515 | 0.81 | 0.88 | 63 | empty |
| 3 | 620 | 0.75 | 0.81 | 58 | YP1 |
| 4 | 516 | 0.74 | 0.82 | 61 | empty |
| 5 | 574 | 0.73 | 0.80 | 78 | empty |
Interfaces
1 interface between chains.
- A–B · 2699 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7DD5 · Structure of Calcium-Sensing Receptor in complex with NPS-2143 · 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
- Elsewhere: RCSB PDB 7DD5 · PDBe 7DD5
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