[English] 日本語
Yorodumi
- PDB-3uzc: Thermostabilised Adenosine A2A receptor in complex with 4-(3-amin... -

+
Open data


ID or keywords:

Loading...

no data

-
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 / homologyG-protein coupled receptors family 1 signature. / Adenosine A2A receptor / G protein-coupled receptor, rhodopsin-like / 7 transmembrane receptor (rhodopsin family) / G-protein coupled receptors family 1 profile. / GPCR, rhodopsin-like, 7TM / Adenosine receptor / NGF-independant TRKA activation / Adenosine P1 receptors / G alpha (s) signalling events ...G-protein coupled receptors family 1 signature. / Adenosine A2A receptor / G protein-coupled receptor, rhodopsin-like / 7 transmembrane receptor (rhodopsin family) / G-protein coupled receptors family 1 profile. / GPCR, rhodopsin-like, 7TM / Adenosine receptor / NGF-independant TRKA activation / Adenosine P1 receptors / G alpha (s) signalling events / Surfactant metabolism / positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / negative regulation of locomotion / G protein-coupled adenosine receptor activity / negative regulation of alpha-beta T cell activation / sensory perception / synaptic transmission, dopaminergic / regulation of norepinephrine secretion / positive regulation of urine volume / positive regulation of renal sodium excretion / eating behavior / synaptic transmission, cholinergic / inhibitory postsynaptic potential / positive regulation of glutamate secretion / protein kinase C-activating G protein-coupled receptor signaling pathway / blood circulation / intermediate filament / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / membrane depolarization / axolemma / positive regulation of apoptotic signaling pathway / synaptic transmission, glutamatergic / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / presynaptic active zone / alpha-actinin binding / vasodilation / excitatory postsynaptic potential / regulation of calcium ion transport / response to caffeine / adenylate cyclase-activating G protein-coupled receptor signaling pathway / phagocytosis / positive regulation of synaptic transmission, glutamatergic / integral component of postsynaptic membrane / prepulse inhibition / cellular defense response / response to amphetamine / central nervous system development / positive regulation of protein secretion / astrocyte activation / locomotory behavior / regulation of mitochondrial membrane potential / negative regulation of protein kinase activity / neuron projection morphogenesis / integral component of presynaptic membrane / negative regulation of inflammatory response / regulation of synaptic vesicle exocytosis / positive regulation of synaptic transmission, GABAergic / positive regulation of long-term synaptic potentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell-cell signaling / negative regulation of neuron apoptotic process / postsynaptic density / blood coagulation / inflammatory response / Golgi membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / glutamatergic synapse / dendrite / apoptotic process / neuronal cell body / regulation of transcription, DNA-templated / cellular protein metabolic process / protein heterodimerization activity / integral component of plasma membrane / enzyme binding / membrane / identical protein binding / plasma membrane / Adenosine receptor A2a
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.341 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2011 / Release: Mar 21, 2012

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine A2A Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7782
Polyers36,4791
Non-polymers2991
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MI 2 2 2

-
Components

#1: Protein/peptide 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: (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 / Formula: C15H11ClN4O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.39 / Density percent sol: 77.2 %
Crystal growTemp: 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

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: May 12, 2010
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI (111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 97.8 Å2 / D resolution high: 3.34 Å / D resolution low: 49.29 Å / Number all: 10975 / Number obs: 10975 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.095 / NetI over sigmaI: 8 / Redundancy: 5.4 % / Percent possible obs: 94.4
Reflection shellRmerge I obs: 0.851 / Highest resolution: 3.34 Å / Lowest resolution: 3.52 Å / MeanI over sigI obs: 1.6 / Number unique all: 1611 / Redundancy: 5.5 % / Percent possible all: 96.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.4_84)refinement
XDSdata reduction
SCALAdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWH
Occupancy max: 1 / Occupancy min: 1 / Overall SU ML: 0.42 / R Free selection details: RANDOM / Sigma F: 1.36 / Overall phase error: 39.97 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 56.799 / Solvent model param ksol: 0.225
Displacement parametersB iso max: 389.77 Å2 / B iso mean: 155.9 Å2 / B iso min: 74.21 Å2 / Aniso B11: 19.3024 Å2 / Aniso B12: - Å2 / Aniso B13: 0 Å2 / Aniso B22: -61.7626 Å2 / Aniso B23: - Å2 / Aniso B33: 42.4601 Å2
Least-squares processR factor R free: 0.2899 / R factor R work: 0.2822 / R factor obs: 0.2825 / Highest resolution: 3.341 Å / Lowest resolution: 19.805 Å / Number reflection R free: 511 / Number reflection all: 10797 / Number reflection obs: 10797 / Percent reflection R free: 4.73 / Percent reflection obs: 92.2
Refine hist #LASTHighest resolution: 3.341 Å / Lowest resolution: 19.805 Å
Number of atoms included #LASTProtein: 2250 / Nucleic acid: 0 / Ligand: 21 / Solvent: 0 / Total: 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
Refine LS shell

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

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.34130.47630.43283.67561282531265993.0000
3.67560.39240.31124.20301322544267692.0000
4.20300.22900.24205.27871132603271693.0000
5.27870.23550.256619.80491382608274691.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.78220.4622-0.23050.37300.33271.8361-0.1385-0.8816-0.25940.93290.89120.01890.0662-0.6210-0.00001.0231-0.01700.07980.70210.06192.047319.896126.422342.3237
20.0116-0.0170-0.00730.01370.0043-0.0001-0.33010.47471.05370.0858-0.24200.16530.11670.94600.00001.66750.25780.14131.06700.00192.913120.892344.570830.3390
30.0143-0.1838-0.26030.58070.82841.1947-0.9074-0.3434-0.0174-1.3947-0.0631-0.34870.8982-0.2434-0.00001.15420.01860.52040.79710.18421.509517.609522.703034.0599
40.23090.0122-0.10180.11030.04280.06420.01150.8587-0.2868-0.89140.66360.06300.70000.11820.00021.7182-0.48130.30041.41880.26403.26777.55854.244732.5211
50.4029-0.02320.53580.0441-0.14340.5634-0.18281.1155-0.2695-1.68560.84800.4586-0.0157-0.80790.00000.9384-0.18080.26000.93720.28332.041721.167323.390924.3474
60.13360.10020.16800.07850.13430.2243-0.86821.28550.6853-1.3287-0.13640.63000.51420.17010.00001.77620.08740.41490.75030.09392.656226.381343.440214.5747
70.8191-0.29080.28330.1084-0.04510.41800.52491.6907-0.5014-1.48770.49020.97950.4425-0.30600.00001.0250-0.0383-0.42250.7615-0.05961.851813.984923.335920.1521
80.1094-0.01240.08270.01330.01900.12080.23060.7374-0.1390-0.2607-0.3527-0.12460.2734-1.0394-0.00021.62940.11600.10541.29590.02332.756713.5006-0.273522.2445
90.0866-0.13820.12490.40350.06160.52611.4071-0.1516-0.4675-1.73580.19611.19801.5934-0.3512-0.00001.4470-0.0032-0.04090.86820.00412.538813.29240.398230.1014
100.9021-0.8373-0.28240.74750.12510.3133-0.32840.17001.3920-0.0231-0.2569-0.5113-0.00530.0241-0.00001.4013-0.26410.08590.87820.17842.175833.910425.924517.8107
110.0374-0.01810.08500.0068-0.03920.19110.4686-0.19360.1141-0.32920.7021-0.66290.9089-0.20570.00001.8685-0.08620.75431.31270.50883.269344.991054.165218.5103
121.87110.1736-1.24050.4612-0.61131.1230-0.58010.7994-0.7424-1.29401.5760-2.6155-0.7585-0.21220.00011.1445-0.0516-0.18050.9679-0.00391.160133.613324.788726.7588
130.2831-0.02220.22080.0883-0.00380.1460-0.0784-0.71300.7774-0.93000.95180.3694-0.78160.71180.00001.0940-0.12920.05930.78690.01283.320732.4025-2.097730.1301
14-0.0895-0.05420.10880.4893-0.32011.7409-0.1174-0.94650.14480.9190-0.1173-0.4923-0.61540.61931.34190.23230.0443-1.33960.8151-0.2153-1.486629.338721.900937.3562
150.1290-0.0107-0.04800.0934-0.12170.1179-0.3614-0.53411.15451.6046-0.0558-1.0137-2.27351.73300.00001.0979-0.0171-0.34060.8537-0.00221.821025.927742.785642.7276
Refine TLS group

Beg auth asym ID: A / End auth asym ID: A / Refine ID: X-RAY DIFFRACTION

IDBeg auth seq IDEnd auth seq IDRefine TLS IDSelection details
17331chain A and resid 7:33
234402chain A and resid 34:40
341683chain A and resid 41:68
469764chain A and resid 69:76
5771045chain A and resid 77:104
61051186chain A and resid 105:118
71191417chain A and resid 119:141
81421498chain A and resid 142:149
91581759chain A and resid 158:175
1017621110chain A and resid 176:211
1121222011chain A and resid 212:220
1222125812chain A and resid 221:258
1325926713chain A and resid 259:267
1426829214chain A and resid 268:292
1529330515chain A and resid 293:305

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more