8TF5

Crystal structure of orphan G protein-coupled receptor 6, pseudoapo form

PDB DOI: https://doi.org/10.2210/pdb8TF5/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2023-07-07 Released: 2024-12-04
Deposition Author(s): Barekatain, M., Johansson, L., Lam, J.H., Sadybekov, A.V., Han, G.W., Popov, P., Russo, J., Bliesath, J., Brice, N., Beresford, M., Carlson, L., Saikatendu, K.S., Sun, H., Murphy, S., Monenschein, H., Schiffer, H.H., Lutomski, C., Robinson, C.V., Liu, Z., Hua, T., Katritch, V., Cherezov, V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.214
R-Value Work: 0.184
R-Value Observed: 0.186

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights into the high basal activity and inverse agonism of the orphan receptor GPR6 implicated in Parkinson's disease

Barekatain, M., Johansson, L., Lam, J.H., Sadybekov, A.V., Han, G.W., Popov, P., Russo, J., Bliesath, J., Brice, N., Beresford, M., Carlson, L., Saikatendu, K.S., Sun, H., Murphy, S., Monenschein, H., Schiffer, H.H., Lutomski, C., Robinson, C.V., Liu, Z., Hua, T., Katritch, V., Cherezov, V.

(2024) Sci Signal

DOI: https://doi.org/10.1126/scisignal.ado8741

Macromolecule Content

Total Structure Weight: 53.82 kDa
Atom Count: 3,312
Modelled Residue Count: 364
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 6,Soluble cytochrome b562 chimera,Soluble cytochrome b562,G-protein coupled receptor 6	A	436	Homo sapiens, Escherichia coli	Mutation(s): 9 Gene Names: GPR6, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P46095 (Homo sapiens) Explore P46095 Go to UniProtKB: P46095
PHAROS: P46095 GTEx: ENSG00000146360
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P46095
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
OLC (Subject of Investigation/LOI) Query on OLC Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A]	B [auth A], C [auth A], L [auth A], M [auth A], O [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A]
P15 (Subject of Investigation/LOI) Query on P15 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]
OLA (Subject of Investigation/LOI) Query on OLA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain P [auth A] SDF format, chain S [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth A]	E [auth A] G [auth A] H [auth A] I [auth A] J [auth A] E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]