5X2O
Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-arginine
- PDB DOI: https://doi.org/10.2210/pdb5X2O/pdb
- Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
- Organism(s): Oryzias latipes, Mus musculus
- Expression System: Drosophila melanogaster, Mus musculus
- Mutation(s): No 
- Deposited: 2017-02-02 Released: 2017-05-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.272 
- R-Value Work: 0.185 
- R-Value Observed: 0.189 
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Taste receptor, type 1, member 2a | 461 | Oryzias latipes | Mutation(s): 0  Gene Names: TAS1R2a | ||
UniProt | |||||
Find proteins for A0A173M0G2 (Oryzias latipes) Explore A0A173M0G2  Go to UniProtKB:  A0A173M0G2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A173M0G2 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Taste receptor, type 1, member 3 | 478 | Oryzias latipes | Mutation(s): 0  Gene Names: TAS1R3 | ||
UniProt | |||||
Find proteins for A0A173M094 (Oryzias latipes) Explore A0A173M094  Go to UniProtKB:  A0A173M094 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A173M094 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab16A Heavy chain | E [auth H], G [auth J] | 225 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab16A Light chain | F [auth L], H [auth K] | 217 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ARG Query on ARG | JA [auth C], P [auth A], QA [auth D], Z [auth B] | ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O | |||
CA Query on CA | TA [auth K] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | AA [auth B], SA [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | KA [auth C], LA [auth C], Q [auth A], R [auth A], RA [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.272 
- R-Value Work: 0.185 
- R-Value Observed: 0.189 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 98.905 | α = 90 |
b = 113.677 | β = 92.23 |
c = 128.636 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-05-24  Deposition Author(s): Nuemket, N., Yasui, N., Atsumi, N., Yamashita, A.
Revision History (Full details and data files)
- Version 1.0: 2017-05-24
Type: Initial release - Version 1.1: 2017-06-21
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary