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Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with L-arginine
Analyse Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X2O
- Type
- protein
- Length
- 2,611 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
- ARG, NAG, NA, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taste receptor, type 1, member 2A | protein | 421 | 35% helix, 21% strand | A0A173M0G2 |
| B | Taste receptor, type 1, member 3 | protein | 452 | 40% helix, 21% strand | A0A173M094 |
| C | Taste receptor, type 1, member 2A | protein | 426 | 35% helix, 21% strand | A0A173M0G2 |
| D | Taste receptor, type 1, member 3 | protein | 441 | 39% helix, 22% strand | A0A173M094 |
| H | FAB16A heavy chain | protein | 219 | 7% helix, 52% strand | — |
| L, K | FAB16A light chain | protein | 216 | 5% helix, 56% strand | — |
| J | FAB16A heavy chain | protein | 220 | 10% helix, 52% strand | — |
Ligands and binding sites
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, D, B, C
- NA · Sodium ion · metal · 5 copies · chains A, C, D
- CA · Calcium ion · metal · chains K
- CL · Chloride ion · ion · 2 copies · chains B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.86 | 0.87 | 127 | ARG |
| 2 | 1028 | 0.86 | 0.87 | 130 | ARG |
| 3 | 282 | 0.78 | 0.90 | 39 | ARG |
| 4 | 524 | 0.75 | 0.83 | 53 | ARG, CL |
| 5 | 68 | 0.74 | 0.98 | 20 | empty |
Interfaces
10 interfaces between chains.
- H–L · 2025 Ų buried · 28 hydrogen bonds · protein-protein
- J–K · 1996 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1870 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 761 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 5X2O · 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 5X2O · PDBe 5X2O · UniProt A0A173M0G2 · UniProt A0A173M094
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