MolNFT v1 · #139034 · protein
Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with glycine
5X2Q · Taste receptor, type 1, member 2A: “Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with glycine”. X-ray diffraction, 6 ligands (GLY, NAG, BMA), 20 pockets (best druggability 0.86).…
- PDB
- 5X2Q
- Type
- protein
- Length
- 2,622 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taste receptor, type 1, member 2A; Taste receptor, type 1, member 3; FAB16A heavy chain…
- UniProt
- A0A173M0G2, A0A173M094
- Ligands
- GLY, NAG, BMA, NA, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taste receptor, type 1, member 2A | protein | 421 | 34% helix, 21% strand | A0A173M0G2 |
| B | Taste receptor, type 1, member 3 | protein | 449 | 40% helix, 22% strand | A0A173M094 |
| C | Taste receptor, type 1, member 2A | protein | 431 | 34% helix, 20% strand | A0A173M0G2 |
| D | Taste receptor, type 1, member 3 | protein | 451 | 40% helix, 22% strand | A0A173M094 |
| H | FAB16A heavy chain | protein | 219 | 8% helix, 51% strand | — |
| L | FAB16A light chain | protein | 217 | 6% helix, 53% strand | — |
| J | FAB16A heavy chain | protein | 218 | 8% helix, 53% strand | — |
| K | FAB16A light chain | protein | 216 | 6% helix, 53% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · 5 copies · chains A, C, D
- CA · Calcium ion · metal · chains K
- CL · Chloride ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.86 | 0.89 | 96 | GLY, CL |
| 2 | 472 | 0.83 | 0.90 | 73 | GLY |
| 3 | 519 | 0.83 | 0.89 | 85 | GLY, CL |
| 4 | 267 | 0.78 | 0.91 | 40 | GLY |
| 5 | 342 | 0.77 | 0.88 | 47 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2039 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1981 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1967 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1872 Ų buried · 13 hydrogen bonds · protein-protein
- C–J · 827 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 5X2Q · Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in… · 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
- Every structure of UniProt A0A173M0G2
- Every structure of UniProt A0A173M094
- Elsewhere: RCSB PDB 5X2Q · PDBe 5X2Q · UniProt A0A173M0G2 · UniProt A0A173M094
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