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- PDB-5x72: The crystal Structure PDE delta in complex with (rac)-p9 -

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Basic information

Entry
Database: PDB / ID: 5x72
TitleThe crystal Structure PDE delta in complex with (rac)-p9
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cilium / cytoplasm / cytosol
Similarity search - Function
GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Chem-P59 / Chem-P69 / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJiang, Y. / Zhuang, C. / Chen, L. / Wang, R. / Wang, F. / Sheng, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China2014CB541800 China
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structural Biology-Inspired Discovery of Novel KRAS-PDE delta Inhibitors
Authors: Jiang, Y. / Zhuang, C. / Chen, L. / Lu, J. / Dong, G. / Miao, Z. / Zhang, W. / Li, J. / Sheng, C.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0783
Polymers17,4411
Non-polymers6372
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8090 Å2
Unit cell
Length a, b, c (Å)55.568, 55.568, 115.465
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

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Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17440.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43924
#2: Chemical ChemComp-P59 / (2R)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one


Mass: 318.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15FN2O
#3: Chemical ChemComp-P69 / (2S)-2-(2-fluorophenyl)-3-phenyl-1,2-dihydroquinazolin-4-one


Mass: 318.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15FN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 15663 / % possible obs: 99.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Χ2: 0.975 / Net I/σ(I): 38.61
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 7.4 / Num. unique obs: 774 / Rpim(I) all: 0.132 / Χ2: 0.935 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JV6

4jv6


Resolution: 1.95→48.12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.541 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23142 742 4.9 %RANDOM
Rwork0.18748 ---
obs0.18968 14524 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å2-0 Å2
2---0.12 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.95→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 48 86 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021307
X-RAY DIFFRACTIONr_bond_other_d0.0020.021233
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.9991764
X-RAY DIFFRACTIONr_angle_other_deg0.9713.0072828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5725149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.94723.93461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.844159
X-RAY DIFFRACTIONr_chiral_restr0.1310.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3721.344599
X-RAY DIFFRACTIONr_mcbond_other1.3731.343598
X-RAY DIFFRACTIONr_mcangle_it2.1681.998744
X-RAY DIFFRACTIONr_mcangle_other2.1661.998745
X-RAY DIFFRACTIONr_scbond_it2.1841.713706
X-RAY DIFFRACTIONr_scbond_other2.1821.715707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4812.4711019
X-RAY DIFFRACTIONr_long_range_B_refined6.07212.541492
X-RAY DIFFRACTIONr_long_range_B_other6.0712.5531493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 47 -
Rwork0.213 800 -
obs--73.52 %
Refinement TLS params.Method: refined / Origin x: -19.8722 Å / Origin y: 19.8937 Å / Origin z: 125.9501 Å
111213212223313233
T0.0571 Å20.0484 Å2-0.0004 Å2-0.0962 Å20.0135 Å2--0.0453 Å2
L2.8292 °2-0.7191 °23.177 °2-0.4263 °2-1.2108 °2--4.428 °2
S0.2971 Å °0.3261 Å °-0.1865 Å °-0.1447 Å °-0.1789 Å °-0.0289 Å °0.4802 Å °0.4525 Å °-0.1182 Å °

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