MolNFT v1 · #139031 · protein
Crystal structure of the medaka fish taste receptor T1R2A-T1R3 ligand binding domains in complex with L-alanine
5X2N · 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, 4 ligands (ALA, NAG, NA), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5X2N
- Type
- protein
- Length
- 2,641 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
- ALA, NAG, NA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 29% 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 | 459 | 38% helix, 21% strand | A0A173M094 |
| C | Taste receptor, type 1, member 2A | protein | 433 | 35% helix, 21% strand | A0A173M0G2 |
| D | Taste receptor, type 1, member 3 | protein | 446 | 39% helix, 21% strand | A0A173M094 |
| H | FAB16A heavy chain | protein | 223 | 9% helix, 50% strand | — |
| L, K | FAB16A light chain | protein | 216 | 6% helix, 53% strand | — |
| J | FAB16A heavy chain | protein | 219 | 7% helix, 53% strand | — |
Ligands and binding sites
- ALA · Alanine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.86 | 0.87 | 119 | ALA |
| 2 | 1076 | 0.85 | 0.86 | 103 | ALA |
| 3 | 510 | 0.77 | 0.84 | 55 | ALA |
| 4 | 489 | 0.76 | 0.84 | 61 | ALA |
| 5 | 98 | 0.75 | 0.96 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1985 Ų buried · 19 hydrogen bonds · protein-protein
- J–K · 1946 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1878 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1776 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 878 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 22 disulfide (N-glycosylation, disulfide).
Compared structures
- 5X2N · 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 5X2N · PDBe 5X2N · UniProt A0A173M0G2 · UniProt A0A173M094
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