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- PDB-7pae: The crystal structure of Deltarasin in complex with PDE6D -

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Basic information

Entry
Database: PDB / ID: 7pae
TitleThe crystal structure of Deltarasin in complex with PDE6D
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsPROTEIN BINDING / inhibitor / complex
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton / cytoplasm / cytosol
Similarity search - Function
Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
ACETIC ACID / deltarasin / 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: 1.85 Å
AuthorsBeaumont, E. / Williams, D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA202756
CitationJournal: Blood Cancer J / Year: 2022
Title: Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. ...Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. / Williams, D.A. / Xu, H.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,0173
Polymers19,3531
Non-polymers6642
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.843, 55.843, 116.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-419-

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: 19352.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O43924
#2: Chemical ChemComp-O7T / deltarasin / 2-phenyl-1-[(1~{S})-2-[4-[1-(phenylmethyl)benzimidazol-2-yl]phenoxy]-1-piperidin-4-yl-ethyl]benzimidazole


Mass: 603.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H37N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.61 % / Description: hexagonal rods
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.8 / Details: 0.1M Na acetate pH3.8, PEG300 29.50% / PH range: 3.6-4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→48.36 Å / Num. obs: 18659 / % possible obs: 99.8 % / Redundancy: 9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.039 / Rrim(I) all: 0.086 / Net I/σ(I): 11.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4623 / CC1/2: 0.725 / Rpim(I) all: 0.484 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
DIALSdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NAL

5nal


Resolution: 1.85→48.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.216 943 5.07 %RANDOM
Rwork0.203 ---
obs0.203 18615 100 %-
Displacement parametersBiso max: 110.66 Å2 / Biso mean: 38.13 Å2 / Biso min: 21.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.5835 Å20 Å20 Å2
2---5.5835 Å20 Å2
3---11.1669 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.85→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 50 127 1395
Biso mean--37.77 45.88 -
Num. residues----149
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d460SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes238HARMONIC5
X-RAY DIFFRACTIONt_it1317HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion159SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1500SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1317HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1780HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion16.45
LS refinement shellResolution: 1.85→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
RfactorNum. reflection% reflection
Rfree0.2831 14 3.53 %
Rwork0.2241 383 -
all0.2259 397 -
obs--98.97 %

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