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- PDB-3tvx: The structure of PDE4A with pentoxifylline at 2.84A resolution -

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Basic information

Entry
Database: PDB / ID: 3tvx
TitleThe structure of PDE4A with pentoxifylline at 2.84A resolution
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 3',5'-cyclic-AMP phosphodiesterase / regulation of protein kinase A signaling / extrinsic component of membrane / cAMP catabolic process / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / cAMP binding / ruffle membrane / sensory perception of smell ...regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 3',5'-cyclic-AMP phosphodiesterase / regulation of protein kinase A signaling / extrinsic component of membrane / cAMP catabolic process / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / cAMP binding / ruffle membrane / sensory perception of smell / cellular response to xenobiotic stimulus / G alpha (s) signalling events / G protein-coupled receptor signaling pathway / perinuclear region of cytoplasm / signal transduction / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / 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. ...Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / 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. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PNX / 3',5'-cyclic-AMP phosphodiesterase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBadger, J. / Sridhar, V.
CitationJournal: J Biomol Screen / Year: 2012
Title: Fragment-Based Screening for Inhibitors of PDE4A Using Enthalpy Arrays and X-ray Crystallography.
Authors: Recht, M.I. / Sridhar, V. / Badger, J. / Hernandez, L. / Chie-Leon, B. / Nienaber, V. / Torres, F.E.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4A
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,47210
Polymers77,5442
Non-polymers9288
Water0
1
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1404
Polymers38,7721
Non-polymers3683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3326
Polymers38,7721
Non-polymers5605
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.938, 104.938, 163.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein cAMP-specific 3',5'-cyclic phosphodiesterase 4A / DPDE2 / PDE46


Mass: 38772.102 Da / Num. of mol.: 2 / Fragment: Catalytic domain residues 351-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4A, DPDE2 / Production host: Escherichia coli (E. coli)
References: UniProt: P27815, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PNX / 3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE / PENTOXIFYLLINE / Pentoxifylline


Mass: 278.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 2ul of 34mg/ml protein in HEPES pH 7.5 150mM NaCl, 5mM DTT with 2ul of 1.5mM Ammonium sulfate, 0.1 M Bis/Tris propane , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.84→48.4 Å / Num. all: 22313 / Num. obs: 22313 / % possible obs: 100 % / Observed criterion σ(F): -4 / Redundancy: 9.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 34.4
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I8V

3i8v


Resolution: 2.84→48.4 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 14.717 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28951 1136 5.1 %RANDOM
Rwork0.22048 ---
obs0.22388 21117 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.118 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.84→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 54 0 5437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215543
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9597529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4295666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59124.783276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00215965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9091530
X-RAY DIFFRACTIONr_chiral_restr0.070.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214190
X-RAY DIFFRACTIONr_mcbond_it0.47323338
X-RAY DIFFRACTIONr_mcangle_it0.8992.55404
X-RAY DIFFRACTIONr_scbond_it0.88732205
X-RAY DIFFRACTIONr_scangle_it1.5074.52125
LS refinement shellResolution: 2.84→2.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 72
Rwork0.274 1523

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