5X2M

Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine

PDB DOI: https://doi.org/10.2210/pdb5X2M/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
Deposition Author(s): Nuemket, N., Yasui, N., Atsumi, N., Yamashita, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.227
R-Value Work: 0.173
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 312.11 kDa
Atom Count: 21,519
Modelled Residue Count: 2,599
Deposited Residue Count: 2,762
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Taste receptor, type 1, member 2a	A, C	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 Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Taste receptor, type 1, member 3	B, D	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 Annotations Expand
Reference Sequence

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Entity ID: 3
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 Annotations Expand
Reference Sequence

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(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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
GLN Query on GLN Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Y [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Y [auth B]	HA [auth C], P [auth A], PA [auth D], Y [auth B]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain HA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain SA [auth L] MOL2 format, chain SA [auth L]	SA [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain SA [auth L] Interactions & Density Focus chain SA [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain RA [auth D] SDF format, chain Z [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain Z [auth B]	RA [auth D], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain RA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain RA [auth D] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D]	IA [auth C], Q [auth A], QA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain Q [auth A] Focus chain QA [auth D] Interactions & Density Focus chain IA [auth C] Focus chain Q [auth A] Focus chain QA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.227
R-Value Work: 0.173
R-Value Observed: 0.176
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.656	α = 90
b = 116.355	β = 92.2
c = 129.476	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

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