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- PDB-10kt: Crystal structure of A2A adenosine receptor A2AR-bRIL in complex ... -

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Entry
Database: PDB / ID: 10kt
TitleCrystal structure of A2A adenosine receptor A2AR-bRIL in complex with Compound50
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Class A GPCR / antagonist
Function / homology
Function and homology information


regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism ...regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / intermediate filament / presynaptic active zone / positive regulation of urine volume / response to caffeine / blood circulation / sensory perception / positive regulation of glutamate secretion / eating behavior / inhibitory postsynaptic potential / regulation of calcium ion transport / alpha-actinin binding / asymmetric synapse / axolemma / membrane depolarization / cellular defense response / prepulse inhibition / phagocytosis / neuron projection morphogenesis / positive regulation of synaptic transmission, glutamatergic / astrocyte activation / presynaptic modulation of chemical synaptic transmission / positive regulation of long-term synaptic potentiation / positive regulation of synaptic transmission, GABAergic / central nervous system development / positive regulation of protein secretion / regulation of mitochondrial membrane potential / response to amphetamine / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / synaptic transmission, glutamatergic / excitatory postsynaptic potential / locomotory behavior / electron transport chain / negative regulation of inflammatory response / vasodilation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / calmodulin binding / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / heme binding / regulation of DNA-templated transcription / lipid binding / dendrite / protein-containing complex binding / glutamatergic synapse / enzyme binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKrishnamurthy, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Med.Chem. / Year: 2026
Title: Discovery of MK-1088 as a Potent A 2A /A 2B Adenosine Receptor Dual-Antagonist for Cancer Immunotherapy.
Authors: Zhang, Y. / Hennessy, E. / Larsen, M.A. / Hao, J. / Pan, J. / Mansoor, U.F. / Sather, A. / Brill, Z.G. / Rico, L. / Swaminathan, U. / Moreno, J. / Vara, B.A. / Ranganath, S. / Palmieri, A. / ...Authors: Zhang, Y. / Hennessy, E. / Larsen, M.A. / Hao, J. / Pan, J. / Mansoor, U.F. / Sather, A. / Brill, Z.G. / Rico, L. / Swaminathan, U. / Moreno, J. / Vara, B.A. / Ranganath, S. / Palmieri, A. / Ogunbodede, O. / Barry, E.R. / Hinton, M.C. / Daublain, P. / Gupta, P. / Chatterjee, M. / Rottey, S. / Presland, J. / Hill, A.D. / Dewey, W.J. / Schneider, S.E. / Ciaccio, P.J. / Otte, K.M. / Rindgen, D. / Tatosian, D. / Turnbull, B.W.H. / Silverman, S.M. / Chobanian, H. / Krishnamurthy, H. / Pang, L. / Wnek, R. / Afshar, R. / Crowley, S. / Miller, A. / O'Neil, J. / Chrencik, J. / Plummer, C.W. / Ali, A. / Cumming, J. / DeMong, D.E.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,25732
Polymers48,1581
Non-polymers9,09931
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.370, 179.380, 140.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562 / Cytochrome b-562


Mass: 48157.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A2A receptor (2-316) with HA signal sequence followed by FLAG tag and GAP at the N-terminus and 8xHis at the C-terminus.,A2A receptor (2-316) with HA signal sequence followed by FLAG tag and ...Details: A2A receptor (2-316) with HA signal sequence followed by FLAG tag and GAP at the N-terminus and 8xHis at the C-terminus.,A2A receptor (2-316) with HA signal sequence followed by FLAG tag and GAP at the N-terminus and 8xHis at the C-terminus.,A2A receptor (2-316) with HA signal sequence followed by FLAG tag and GAP at the N-terminus and 8xHis at the C-terminus.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Plasmid: pBAC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 8 types, 128 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-A1C5S / (4%{S})-2-[(3%{R},6%{S})-1-(1-ethyl-1%{H}-pyrazol-4-yl)-6-methylpiperidin-3-yl]-7-methoxy[1,2,4]triazolo[1,5-%{c}]quinazolin-5-amine


Mass: 406.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Description: small 20uM crystals. Combined 160 mini datasets to obtain the full dataset.
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M sodium citrate buffer pH 5.0, 0.02-0.04 M Na thiocyanate, 27-30% PEG400, and 2% (v/v) 2, 5-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.587→89.69 Å / Num. obs: 29661 / % possible obs: 98.9 % / Redundancy: 20 % / Biso Wilson estimate: 52.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.61
Reflection shellResolution: 2.59→2.65 Å / Num. unique obs: 1009 / CC1/2: 0.096 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.53 Å / SU ML: 0.3225 / Cross valid method: FREE R-VALUE / σ(F): 0.49 / Phase error: 26.4332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 1417 4.78 %
Rwork0.2075 28209 -
obs0.2092 29626 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.46 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 496 97 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393602
X-RAY DIFFRACTIONf_angle_d0.64694806
X-RAY DIFFRACTIONf_chiral_restr0.0382535
X-RAY DIFFRACTIONf_plane_restr0.0041597
X-RAY DIFFRACTIONf_dihedral_angle_d14.42441604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.680.32861200.33412473X-RAY DIFFRACTION86.2
2.68-2.790.39091310.30532905X-RAY DIFFRACTION99.97
2.79-2.910.28431700.28252778X-RAY DIFFRACTION100
2.91-3.070.31821620.27192864X-RAY DIFFRACTION100
3.07-3.260.36341330.25712897X-RAY DIFFRACTION100
3.26-3.510.27521400.20982852X-RAY DIFFRACTION100
3.51-3.860.23661650.19062817X-RAY DIFFRACTION100
3.86-4.420.20631390.15412897X-RAY DIFFRACTION100
4.42-5.570.17571240.17212873X-RAY DIFFRACTION100
5.57-41.530.2061330.19642853X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: -17.761816565916 Å / Origin y: -15.898513620991 Å / Origin z: 18.207970040141 Å
111213212223313233
T0.32892426435071 Å2-0.00069359906448493 Å2-0.013494911543501 Å2-0.35580198546174 Å2-0.00085933405531302 Å2--0.33717095880673 Å2
L0.26857989092192 °20.14364543244696 °20.11332301783525 °2-0.18236717032991 °2-0.044876535215904 °2--0.19608909753317 °2
S-0.0069962459440493 Å °-0.0059315477860892 Å °-0.072231002385852 Å °0.019778691481283 Å °0.042768988104784 Å °-0.03329219319891 Å °-0.01083906090288 Å °-0.015978660912277 Å °2.0728022907438E-5 Å °
Refinement TLS groupSelection details: all

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