8K5D

Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 (Local refinement)

PDB DOI: https://doi.org/10.2210/pdb8K5D/pdb
EM Map EMD-36902: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2023-07-21 Released: 2023-11-22
Deposition Author(s): Park, J.H., Ishimoto, N., Park, S.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2

Park, J.H., Kawakami, K., Ishimoto, N., Ikuta, T., Ohki, M., Ekimoto, T., Ikeguchi, M., Lee, D.S., Lee, Y.H., Tame, J.R.H., Inoue, A., Park, S.Y.

(2023) Nat Commun 14: 7150

DOI: https://doi.org/10.1038/s41467-023-42764-8

Macromolecule Content

Total Structure Weight: 54.58 kDa
Atom Count: 2,345
Modelled Residue Count: 291
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human hydroxycarboxylic acid receptor 2	A	476	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS4 (Homo sapiens) Explore Q8TDS4 Go to UniProtKB: Q8TDS4
PHAROS: Q8TDS4 GTEx: ENSG00000182782
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TDS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OKL (Subject of Investigation/LOI) Query on OKL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	8-chloranyl-3-pentyl-7H-purine-2,6-dione C₁₀ H₁₃ Cl N₄ O₂ CGAMDQCXAAOFSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-22
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.