MolNFT v1 · #139030 · protein
Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with L-glutamine
5X2M · Taste receptor, type 1, member 2A: “Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with…”. X-ray diffraction, 5 ligands (GLN, NAG, NA), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5X2M
- Type
- protein
- Length
- 2,599 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
- GLN, NAG, NA, CA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taste receptor, type 1, member 2A | protein | 429 | 35% helix, 21% strand | A0A173M0G2 |
| B | Taste receptor, type 1, member 3 | protein | 452 | 39% helix, 21% strand | A0A173M094 |
| C | Taste receptor, type 1, member 2A | protein | 427 | 35% helix, 21% strand | A0A173M0G2 |
| D | Taste receptor, type 1, member 3 | protein | 422 | 38% helix, 19% strand | A0A173M094 |
| H | FAB16A heavy chain | protein | 219 | 8% helix, 51% strand | — |
| L | FAB16A light chain | protein | 217 | 4% helix, 55% strand | — |
| J | FAB16A heavy chain | protein | 217 | 8% helix, 53% strand | — |
| K | FAB16A light chain | protein | 216 | 5% helix, 53% strand | — |
Ligands and binding sites
- GLN · Glutamine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, D, B, C
- NA · Sodium ion · metal · 3 copies · chains A, C, D
- CA · Calcium ion · metal · chains L
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.86 | 0.87 | 122 | GLN |
| 2 | 582 | 0.83 | 0.89 | 81 | GLN |
| 3 | 427 | 0.82 | 0.90 | 69 | GLN |
| 4 | 298 | 0.77 | 0.89 | 41 | GLN, CL |
| 5 | 134 | 0.67 | 0.88 | 23 | empty |
Interfaces
8 interfaces between chains.
- H–L · 2011 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1931 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1777 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 13 hydrogen bonds · protein-protein
- C–J · 908 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 5X2M · Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in… · the same entry in another collection · chain H against H, 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 5X2M · PDBe 5X2M · UniProt A0A173M0G2 · UniProt A0A173M094
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