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- PDB-5edh: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH n... -

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Basic information

Entry
Database: PDB / ID: 5edh
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH n4c(C)n1c(nc(n1)CCc2nc(nn2C)N3CCCC3)c(c4)CC, micromolar IC50=0.0037753
ComponentscAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
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-5MF / cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / diffrn_radiation_wavelength / 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

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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)147,78116
Polymers146,0614
Non-polymers1,72112
Water9,476526
1
A: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9454
Polymers36,5151
Non-polymers4303
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)36,9454
Polymers36,5151
Non-polymers4303
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)36,9454
Polymers36,5151
Non-polymers4303
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)36,9454
Polymers36,5151
Non-polymers4303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.401, 135.401, 235.335
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 36515.152 Da / Num. of mol.: 4
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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-5MF / 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine


Mass: 340.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H24N8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.59 %
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: 0.99995 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2.03→43.68 Å / Num. obs: 103725 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.17 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Χ2: 0.988 / Net I/σ(I): 14.8 / Num. measured all: 548572
Reflection shellResolution: 2.03→2.13 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.28 / Num. measured obs: 6324 / Num. possible: 1183 / Num. unique obs: 1173 / CC1/2: 1 / Rrim(I) all: 0.018 / Rsym value: 0.742 / Rejects: 0 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→43.68 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.759 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 5007 5 %RANDOM
Rwork0.186 ---
obs0.188 95000 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80 Å2 / Biso mean: 40.871 Å2 / Biso min: 18.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.37 Å20 Å2
2---0.37 Å2-0 Å2
3---1.2 Å2
Refinement stepCycle: final / Resolution: 2.03→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10166 0 108 526 10800
Biso mean--32.77 40.22 -
Num. residues----1253
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 341 -
Rwork0.367 6422 -
all-6763 -
obs--87.97 %

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