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- PDB-3uzc: Thermostabilised Adenosine A2A receptor in complex with 4-(3-amin... -

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Basic information

Entry
Database: PDB / ID: 3uzc
TitleThermostabilised Adenosine A2A receptor in complex with 4-(3-amino-5-phenyl-1,2,4-triazin-6-yl)-2-chlorophenol
ComponentsAdenosine A2A Receptor
KeywordsSIGNALING PROTEIN / 7TM / GPCR / G-PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / response to inorganic substance / cellular defense response / prepulse inhibition / phagocytosis / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / calmodulin binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / dendrite / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-T4E / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.341 Å
AuthorsCongreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / Zhukov, A. / Weir, M. / Marshall, F.H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of 1,2,4-Triazine Derivatives as Adenosine A(2A) Antagonists using Structure Based Drug Design
Authors: Congreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / Tehan, B. / Zhukov, A. / Weir, M. / Marshall, F.H.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine A2A Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7782
Polymers36,4791
Non-polymers2991
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.700, 112.064, 126.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Adenosine A2A Receptor


Mass: 36479.102 Da / Num. of mol.: 1 / Fragment: residues 1-317 / Mutation: A54L T88A R107A K122A L202A L235A V239A S277A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274
#2: Chemical ChemComp-T4E / 4-(3-amino-5-phenyl-1,2,4-triazin-6-yl)-2-chlorophenol


Mass: 298.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN4O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 5.39 Å3/Da / Density % sol: 77.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32-42% PEG1000, 0.25M MGCL2, 0.3% NG, 0.1%(W/V) 1-BUTANOL, 0.05% CYMAL-6, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2010
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 3.34→49.29 Å / Num. all: 10975 / Num. obs: 10975 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8
Reflection shellResolution: 3.34→3.52 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1611 / % possible all: 96.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.4_84)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWH

3pwh


Resolution: 3.341→19.805 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.36 / Phase error: 39.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 511 4.73 %RANDOM
Rwork0.2822 ---
obs0.2825 10797 92.2 %-
all-10797 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.799 Å2 / ksol: 0.225 e/Å3
Displacement parametersBiso max: 389.77 Å2 / Biso mean: 155.9 Å2 / Biso min: 74.21 Å2
Baniso -1Baniso -2Baniso -3
1-19.3024 Å2-0 Å20 Å2
2---61.7626 Å2-0 Å2
3---42.4601 Å2
Refinement stepCycle: LAST / Resolution: 3.341→19.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 21 0 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022333
X-RAY DIFFRACTIONf_angle_d0.3923180
X-RAY DIFFRACTIONf_chiral_restr0.027377
X-RAY DIFFRACTIONf_plane_restr0.002390
X-RAY DIFFRACTIONf_dihedral_angle_d11.047789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3413-3.67560.47631280.43282531265993
3.6756-4.2030.39241320.31122544267692
4.203-5.27870.2291130.2422603271693
5.2787-19.80490.23551380.25662608274691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78220.4622-0.23050.3730.33271.8361-0.1385-0.8816-0.25940.93290.89120.01890.0662-0.621-01.0231-0.0170.07980.70210.06192.047319.896126.422342.3237
20.0116-0.017-0.00730.01370.0043-0.0001-0.33010.47471.05370.0858-0.2420.16530.11670.94601.66750.25780.14131.0670.00192.913120.892344.570830.339
30.0143-0.1838-0.26030.58070.82841.1947-0.9074-0.3434-0.0174-1.3947-0.0631-0.34870.8982-0.2434-01.15420.01860.52040.79710.18421.509517.609522.70334.0599
40.23090.0122-0.10180.11030.04280.06420.01150.8587-0.2868-0.89140.66360.0630.70.11820.00021.7182-0.48130.30041.41880.2643.26777.55854.244732.5211
50.4029-0.02320.53580.0441-0.14340.5634-0.18281.1155-0.2695-1.68560.8480.4586-0.0157-0.807900.9384-0.18080.260.93720.28332.041721.167323.390924.3474
60.13360.10020.1680.07850.13430.2243-0.86821.28550.6853-1.3287-0.13640.630.51420.170101.77620.08740.41490.75030.09392.656226.381343.440214.5747
70.8191-0.29080.28330.1084-0.04510.4180.52491.6907-0.5014-1.48770.49020.97950.4425-0.30601.025-0.0383-0.42250.7615-0.05961.851813.984923.335920.1521
80.1094-0.01240.08270.01330.0190.12080.23060.7374-0.139-0.2607-0.3527-0.12460.2734-1.0394-0.00021.62940.1160.10541.29590.02332.756713.5006-0.273522.2445
90.0866-0.13820.12490.40350.06160.52611.4071-0.1516-0.4675-1.73580.19611.1981.5934-0.3512-01.447-0.0032-0.04090.86820.00412.538813.29240.398230.1014
100.9021-0.8373-0.28240.74750.12510.3133-0.32840.171.392-0.0231-0.2569-0.5113-0.00530.0241-01.4013-0.26410.08590.87820.17842.175833.910425.924517.8107
110.0374-0.01810.0850.0068-0.03920.19110.4686-0.19360.1141-0.32920.7021-0.66290.9089-0.205701.8685-0.08620.75431.31270.50883.269344.99154.165218.5103
121.87110.1736-1.24050.4612-0.61131.123-0.58010.7994-0.7424-1.2941.576-2.6155-0.7585-0.21220.00011.1445-0.0516-0.18050.9679-0.00391.160133.613324.788726.7588
130.2831-0.02220.22080.0883-0.00380.146-0.0784-0.7130.7774-0.930.95180.3694-0.78160.711801.094-0.12920.05930.78690.01283.320732.4025-2.097730.1301
14-0.0895-0.05420.10880.4893-0.32011.7409-0.1174-0.94650.14480.919-0.1173-0.4923-0.61540.61931.34190.23230.0443-1.33960.8151-0.2153-1.486629.338721.900937.3562
150.129-0.0107-0.0480.0934-0.12170.1179-0.3614-0.53411.15451.6046-0.0558-1.0137-2.27351.73301.0979-0.0171-0.34060.8537-0.00221.82125.927742.785642.7276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 7:33A7 - 33
2X-RAY DIFFRACTION2chain A and resid 34:40A34 - 40
3X-RAY DIFFRACTION3chain A and resid 41:68A41 - 68
4X-RAY DIFFRACTION4chain A and resid 69:76A69 - 76
5X-RAY DIFFRACTION5chain A and resid 77:104A77 - 104
6X-RAY DIFFRACTION6chain A and resid 105:118A105 - 118
7X-RAY DIFFRACTION7chain A and resid 119:141A119 - 141
8X-RAY DIFFRACTION8chain A and resid 142:149A142 - 149
9X-RAY DIFFRACTION9chain A and resid 158:175A158 - 175
10X-RAY DIFFRACTION10chain A and resid 176:211A176 - 211
11X-RAY DIFFRACTION11chain A and resid 212:220A212 - 220
12X-RAY DIFFRACTION12chain A and resid 221:258A221 - 258
13X-RAY DIFFRACTION13chain A and resid 259:267A259 - 267
14X-RAY DIFFRACTION14chain A and resid 268:292A268 - 292
15X-RAY DIFFRACTION15chain A and resid 293:305A293 - 305

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