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- PDB-1xos: Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Si... -

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Basic information

Entry
Database: PDB / ID: 1xos
TitleCatalytic Domain Of Human Phosphodiesterase 4B In Complex With Sildenafil
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4B
KeywordsHYDROLASE / Phosphodiesterase / PDE / PDE4B / Sildenafil / Viagra
Function / homology
Function and homology information


negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration ...negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / excitatory synapse / DARPP-32 events / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / cAMP binding / cellular response to epinephrine stimulus / neutrophil chemotaxis / positive regulation of interleukin-2 production / calcium channel regulator activity / Z disc / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / synaptic vesicle / T cell receptor signaling pathway / cellular response to lipopolysaccharide / dendritic spine / transmembrane transporter binding / postsynaptic density / centrosome / metal ion binding / 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-VIA / 3',5'-cyclic-AMP phosphodiesterase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsCard, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. ...Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J.
CitationJournal: STRUCTURE / Year: 2004
Title: Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases.
Authors: Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / ...Authors: Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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
Remark 600HETEROGEN HOH 1003-1009 ARE ASSOCIATED WITH CHAIN A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,5445
Polymers45,8841
Non-polymers6604
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.571, 107.117, 89.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe biological assembly is one monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein cAMP-specific 3',5'-cyclic phosphodiesterase 4B / DPDE4 / PDE32


Mass: 45883.570 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus(RIL)
References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-VIA / 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE / SILDENAFIL / VIAGRA


Mass: 474.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O4S / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10
Details: ammonium sulfate and lithium sulfate , pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.28→70.71 Å / Num. all: 19916 / Num. obs: 19916 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.8
Reflection shellResolution: 2.28→2.339 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.01084 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→70.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.51 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25683 1080 5.1 %RANDOM
Rwork0.21009 ---
obs0.21245 19916 99.68 %-
all-19916 --
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 mean: 43.618 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2--4.68 Å20 Å2
3----6.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.218 Å0.262 Å
Refinement stepCycle: LAST / Resolution: 2.28→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 40 17 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212691
X-RAY DIFFRACTIONr_bond_other_d0.0020.022388
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9573653
X-RAY DIFFRACTIONr_angle_other_deg1.09935555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022967
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02529
X-RAY DIFFRACTIONr_nbd_refined0.2150.2629
X-RAY DIFFRACTIONr_nbd_other0.2230.22718
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1120.21511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.51608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33722601
X-RAY DIFFRACTIONr_scbond_it1.99631083
X-RAY DIFFRACTIONr_scangle_it3.1854.51052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 78
Rwork0.375 1413
Refinement TLS params.Method: refined / Origin x: 2.562 Å / Origin y: 53.355 Å / Origin z: 42.554 Å
111213212223313233
T0.0262 Å20.0229 Å20.0202 Å2-0.0263 Å20.0353 Å2--0.287 Å2
L0.349 °2-0.2702 °2-0.4179 °2-1.9654 °2-0.9173 °2--4.521 °2
S-0.0585 Å °0.0213 Å °-0.118 Å °0.1356 Å °0.1888 Å °0.1053 Å °-0.1477 Å °-0.303 Å °-0.1302 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA162 - 19332 - 63
2X-RAY DIFFRACTION1AA195 - 31965 - 189
3X-RAY DIFFRACTION1AA321 - 367191 - 237
4X-RAY DIFFRACTION1AA370 - 431240 - 301
5X-RAY DIFFRACTION1AA433 - 485303 - 355

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