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- PDB-1xot: Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Va... -

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Basic information

Entry
Database: PDB / ID: 1xot
TitleCatalytic Domain Of Human Phosphodiesterase 4B In Complex With Vardenafil
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4B
KeywordsHYDROLASE / Phosphodiesterase / PDE / PDE4B / Vardenafil / Levitra
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 / excitatory synapse / DARPP-32 events / 3',5'-cyclic-GMP phosphodiesterase activity / calcium channel regulator activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cellular response to epinephrine stimulus / neutrophil chemotaxis / positive regulation of interleukin-2 production / cAMP-mediated signaling / 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 / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / nucleus / 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-VDN / 3',5'-cyclic-AMP phosphodiesterase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...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: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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
Remark 600HETEROGEN HOH 1003-1008 ARE ASSOCIATED WITH CHAIN A. HOH 2003-2008 ARE ASSOCIATED WITH CHAIN B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,6198
Polymers91,4632
Non-polymers1,1576
Water82946
1
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3104
Polymers45,7311
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3104
Polymers45,7311
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.841, 94.423, 108.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is one monomer.

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Components

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


Mass: 45731.332 Da / Num. of mol.: 2 / 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
#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-VDN / 2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE / VARDENAFIL, LEVITRA


Mass: 488.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N6O4S / Comment: medication, inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
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: Aug 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.34→70.71 Å / Num. all: 37567 / Num. obs: 37567 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.1
Reflection shellResolution: 2.34→2.401 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.3 / % 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: 2.34→70.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.063 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25944 2002 5.1 %RANDOM
Rwork0.21019 ---
obs0.21267 37567 99.58 %-
all-37567 --
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: 25.733 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å20 Å2
2--1.01 Å20 Å2
3---4.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.244 Å0.303 Å
Refinement stepCycle: LAST / Resolution: 2.34→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 72 46 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215410
X-RAY DIFFRACTIONr_bond_other_d0.0020.024808
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9547344
X-RAY DIFFRACTIONr_angle_other_deg0.98311196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2925644
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_restr0.1180.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025946
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021054
X-RAY DIFFRACTIONr_nbd_refined0.2170.21279
X-RAY DIFFRACTIONr_nbd_other0.220.25479
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.23126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.53228
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14225234
X-RAY DIFFRACTIONr_scbond_it2.00832182
X-RAY DIFFRACTIONr_scangle_it3.1214.52110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.38 149
Rwork0.321 2742
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6476-0.666-0.89911.6120.0173.6253-0.0780.0031-0.1635-0.0876-0.1692-0.11440.13760.38430.24720.25160.02650.05330.12390.1510.18642.58192.640752.9873
25.10420.4028-0.16751.41340.08223.1546-0.06610.1883-0.5234-0.0015-0.0470.0510.1704-0.27280.11310.3063-0.01040.07430.1332-0.00160.09522.35662.120153.1913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA163 - 19333 - 63
2X-RAY DIFFRACTION1BA195 - 48565 - 355
3X-RAY DIFFRACTION2AB163 - 19333 - 63
4X-RAY DIFFRACTION2AB195 - 48565 - 355

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