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- PDB-1xoz: Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Ta... -

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Basic information

Entry
Database: PDB / ID: 1xoz
TitleCatalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil
ComponentscGMP-specific 3',5'-cyclic phosphodiesterase
KeywordsHYDROLASE / Phosphodiesterase / PDE / PDE5A / Tadalafil / Cialis
Function / homology
Function and homology information


3',5'-cyclic-GMP phosphodiesterase / RHOBTB1 GTPase cycle / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / Smooth Muscle Contraction / : ...3',5'-cyclic-GMP phosphodiesterase / RHOBTB1 GTPase cycle / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / Smooth Muscle Contraction / : / 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-CIA / cGMP-specific 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 7, 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: Version format compliance
Revision 1.3Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_remark / 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_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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600HETEROGEN HOH 1001-1007 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: cGMP-specific 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3074
Polymers41,8281
Non-polymers4793
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.102, 76.397, 80.699
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is one monomer.

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Components

#1: Protein cGMP-specific 3',5'-cyclic phosphodiesterase / CGB-PDE / cGMP-binding cGMP-specific phosphodiesterase / PDE5A


Mass: 41827.934 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE5A, PDE5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus(RIL)
References: UniProt: O76074, 3',5'-cyclic-nucleotide phosphodiesterase
#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-CIA / 6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A-HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4-DIONE / TADALAFIL / CIALIS


Mass: 389.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Sep 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.37→79.06 Å / Num. all: 64263 / Num. obs: 64263 / % possible obs: 97.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.7
Reflection shellResolution: 1.37→1.406 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 1.4 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→79.06 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.05 / SU ML: 0.041 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19335 3416 5 %RANDOM
Rwork0.15203 ---
obs0.1541 64263 97.38 %-
all-64263 --
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: 10.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.18 Å2
2--0.37 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.06 Å0.062 Å
Refinement stepCycle: LAST / Resolution: 1.37→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 31 352 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212732
X-RAY DIFFRACTIONr_bond_other_d0.0020.022466
X-RAY DIFFRACTIONr_angle_refined_deg1.921.9673681
X-RAY DIFFRACTIONr_angle_other_deg1.11435756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5175325
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_restr0.1990.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
X-RAY DIFFRACTIONr_nbd_refined0.2350.2673
X-RAY DIFFRACTIONr_nbd_other0.2450.22863
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.21523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.370.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3420.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8071.51637
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7922631
X-RAY DIFFRACTIONr_scbond_it4.33131095
X-RAY DIFFRACTIONr_scangle_it6.4534.51050
X-RAY DIFFRACTIONr_rigid_bond_restr2.41122732
X-RAY DIFFRACTIONr_sphericity_free6.5522351
X-RAY DIFFRACTIONr_sphericity_bonded3.39822669
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 243
Rwork0.33 4453
Refinement TLS params.Method: refined / Origin x: 37.033 Å / Origin y: 39.879 Å / Origin z: 20.528 Å
111213212223313233
T0.0375 Å2-0.0047 Å20.0375 Å2-0.0214 Å20.0094 Å2--0.0906 Å2
L1.1966 °2-0.1052 °2-0.1537 °2-0.5414 °20.0851 °2--0.6899 °2
S0.0014 Å °-0.0359 Å °0.0425 Å °0.0015 Å °0.0042 Å °0.0175 Å °-0.0308 Å °-0.0447 Å °-0.0056 Å °

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