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- PDB-5ml4: The crystal structure of PDE6D in complex to inhibitor-7 -

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Basic information

Entry
Database: PDB / ID: 5ml4
TitleThe crystal structure of PDE6D in complex to inhibitor-7
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / Prenyl binding protein / farnesylated KRas / Plasmam membrane / Arl2
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cytosol / cytoplasm
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-RRQ / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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)17,9992
Polymers17,3101
Non-polymers6891
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.950, 55.950, 115.300
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-RRQ / 4-[[[4-[(4-chlorophenyl)methyl-cyclopentyl-sulfamoyl]phenyl]sulfonyl-(piperidin-4-ylmethyl)amino]methyl]-2-(methylamino)benzoic acid


Mass: 689.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41ClN4O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.4 M NaOAc, 0.1 M NaCAC, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.4→27.98 Å / Num. obs: 8200 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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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: 2.4→27.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.75 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.248
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 432 5 %RANDOM
Rwork0.1853 ---
obs0.1886 8200 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.94 Å2 / Biso mean: 28.103 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.48 Å2-0 Å2
2--0.48 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: final / Resolution: 2.4→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 46 63 1309
Biso mean--33.15 30.45 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021276
X-RAY DIFFRACTIONr_bond_other_d0.0030.021219
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9911726
X-RAY DIFFRACTIONr_angle_other_deg0.9193.0132801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4635148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.37723.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.01159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 31 -
Rwork0.202 596 -
all-627 -
obs--100 %

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