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- PDB-5ml3: The crystal structure of PDE6D in complex to Deltasonamide1 -

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Basic information

Entry
Database: PDB / ID: 5ml3
TitleThe crystal structure of PDE6D in complex to Deltasonamide1
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / Prenyl binding protein / farnesylated KRas / plasma membrane / Arl2
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / 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-DL3 / 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: 1.4 Å
AuthorsFansa, E.K. / Martin-Gago, P. / Waldmann, H. / Wittinghofer, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
SFBSFB 642 Germany
European Research CouncilERC Grant 268782 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
Authors: Martin-Gago, P. / Fansa, E.K. / Klein, C.H. / Murarka, S. / Janning, P. / Schurmann, M. / Metz, M. / Ismail, S. / Schultz-Fademrecht, C. / Baumann, M. / Bastiaens, P.I. / Wittinghofer, A. / Waldmann, H.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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)17,9572
Polymers17,3101
Non-polymers6471
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.010, 56.010, 115.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 17309.793 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 (E. coli) / References: UniProt: O43924
#2: Chemical ChemComp-DL3 / ~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide


Mass: 647.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H39ClN6O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaOAc, 0.1 M Na3Cit, pH 5.5, 10 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→44.7 Å / Num. obs: 39854 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.5
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 1.4→44.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.908 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2098 5 %RANDOM
Rwork0.1891 ---
obs0.1898 39854 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.31 Å2 / Biso mean: 20.788 Å2 / Biso min: 10.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.36 Å2-0 Å2
2--0.36 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 1.4→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 43 180 1416
Biso mean--21.73 33.46 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021320
X-RAY DIFFRACTIONr_bond_other_d0.0030.021276
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9851792
X-RAY DIFFRACTIONr_angle_other_deg0.9983.0132934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2622.95161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86115235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3451512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 153 -
Rwork0.267 2902 -
all-3055 -
obs--99.97 %

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