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- PDB-5edg: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c... -

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Basic information

Entry
Database: PDB / ID: 5edg
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c1(c(nc([nH]1)Cl)c2ccccc2)C4=NN(c3cccc(c3)OC(F)(F)F)C=CC4=O, micromolar IC50=0.029618
Components(cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase ...) x 2
KeywordsHYDROLASE / PHOSPHODIESTERASE / PDE10
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cAMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding ...extrinsic component of postsynaptic density membrane / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cAMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / cAMP binding / G alpha (s) signalling events / perikaryon / glutamatergic synapse / metal ion binding / cytosol
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5MG / cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJoseph, C. / Rudolph, M.G.
CitationJournal: J.Med.Chem. / Year: 2016
Title: A Real-World Perspective on Molecular Design.
Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
B: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
C: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
D: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,27816
Polymers146,1884
Non-polymers2,09012
Water5,747319
1
A: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0524
Polymers36,5291
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1234
Polymers36,6001
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0524
Polymers36,5291
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0524
Polymers36,5291
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.148, 135.148, 235.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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CAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase ... , 2 types, 4 molecules ACDB

#1: Protein cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A


Mass: 36529.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase
#2: Protein cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A


Mass: 36600.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase

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Non-polymers , 4 types, 331 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-5MG / 3-(2-chloranyl-5-phenyl-1~{H}-imidazol-4-yl)-1-[3-(trifluoromethyloxy)phenyl]pyridazin-4-one


Mass: 432.783 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H12ClF3N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES/NaOH pH 7.5, 30% PEG550MME, 50mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0075 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0075 Å / Relative weight: 1
ReflectionResolution: 2.3→43.47 Å / Num. obs: 70979 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.89 % / Biso Wilson estimate: 53.473 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.09 / Χ2: 0.972 / Net I/σ(I): 13.06 / Num. measured all: 276413
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.361.1221.2820109521752090.3441.30999.8
2.36-2.420.8821.5719897512851230.5481.02699.9
2.42-2.490.7991.819376499349910.5780.928100
2.49-2.570.5692.4318762484848420.7050.66299.9
2.57-2.660.4473.0718312470347000.8070.51999.9
2.66-2.750.3633.8617559451845140.8550.42199.9
2.75-2.850.2874.7217085439043870.9130.33499.9
2.85-2.970.2216.1116405419841970.9510.257100
2.97-3.10.1697.8515782403040270.9710.19699.9
3.1-3.250.12510.6315281391539080.9830.14499.8
3.25-3.430.08414.7714288366236580.9920.09899.9
3.43-3.640.06319.5813565347534710.9950.07399.9
3.64-3.890.05124.0612607327332620.9970.05999.7
3.89-4.20.03929.511711301930110.9980.04599.7
4.2-4.60.03233.7511100283728370.9990.037100
4.6-5.140.0337.019790250024990.9980.035100
5.14-5.940.0335.48816223622360.9990.035100
5.94-7.270.02837.87409188918850.9990.03399.8
7.27-10.290.01949.235672145414510.9990.02299.8
10.290.02152.6828877987710.9990.02496.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementResolution: 2.3→41.47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.241 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 3394 5 %RANDOM
Rwork0.2124 ---
obs0.2148 64873 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80 Å2 / Biso mean: 40.211 Å2 / Biso min: 16.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.33 Å20 Å2
2---0.67 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 2.3→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10178 0 128 319 10625
Biso mean--54.33 40.14 -
Num. residues----1254
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 259 -
Rwork0.376 4414 -
all-4673 -
obs--89.74 %

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