6WQA

2.0A angstrom A2a adenosine receptor structure using XFEL data collected in helium atmosphere.

PDB DOI: https://doi.org/10.2210/pdb6WQA/pdb

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

Deposited: 2020-04-28 Released: 2020-11-18
Deposition Author(s): Lee, M.-Y., Geiger, J., Ishchenko, A., Han, G.W., Barty, A., White, T.A., Gati, C., Batyuk, A., Hunter, M.S., Aquila, A., Boutet, S., Weierstall, U., Cherezov, V., Liu, W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.216
R-Value Work: 0.193
R-Value Observed: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Lee, M.-Y., Geiger, J., Ishchenko, A., Han, G.W., Barty, A., White, T.A., Gati, C., Batyuk, A., Hunter, M.S., Aquila, A., Boutet, S., Weierstall, U., Cherezov, V., Liu, W.

(2020) IUCrJ 7: 976-984

DOI: https://doi.org/10.1107/S2052252520012701

Macromolecule Content

Total Structure Weight: 57.96 kDa
Atom Count: 3,477
Modelled Residue Count: 391
Deposited Residue Count: 447
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine receptor A2a/Soluble cytochrome b562 chimera	A	447	Homo sapiens, Escherichia coli	Mutation(s): 0 Gene Names: ADORA2A, ADORA2, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for P29274 (Homo sapiens) Explore P29274 Go to UniProtKB: P29274
PHAROS: P29274 GTEx: ENSG00000128271
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P29274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	D [auth A], Q [auth A], R [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain D [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain D [auth A] Focus chain Q [auth A] Focus chain R [auth A]
OLB Query on OLB Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-QJRAZLAKSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] SDF format, chain S [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth A]	AA [auth A], BA [auth A], L [auth A], P [auth A], S [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain S [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain S [auth A]
ZMA Query on ZMA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol C₁₆ H₁₅ N₇ O₂ PWTBZOIUWZOPFT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth A], O [auth A], T [auth A], U [auth A], V [auth A], W [auth A], Y [auth A], Z [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain E [auth A] Focus chain F [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 M [auth A] Focus chain O [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [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 M [auth A] Focus chain O [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMA	BindingDB: 6WQA	Ki: min: 0.1, max: 395 (nM) from 18 assay(s)
		Kd: min: 0.22, max: 286 (nM) from 2 assay(s)
		IC50: min: 0.68, max: 81 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.216
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.35	α = 90
b = 180.5	β = 90
c = 142.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM127086

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary