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- PDB-4jvf: The Crystal structure of PDE6D in complex with the inhibitor (s)-5 -

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Basic information

Entry
Database: PDB / ID: 4jvf
TitleThe Crystal structure of PDE6D in complex with the inhibitor (s)-5
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsProtein binding/inhibitor / Immunoglobulin-like beta-sandwich / GDI-like solubilizing factor / Prenyl binding / Protein binding-inhibitor complex
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 / cytoskeleton / cilium / intracellular membrane-bounded organelle ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle / 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-17X / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGunther, Z. / Papke, B. / Ismail, S. / Vartak, N. / Chandra, A. / Hoffmann, M. / Hahn, S. / Triola, G. / Wittinghofer, A. / Bastiaens, P. / Waldmann, H.
CitationJournal: Nature / Year: 2013
Title: Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
Authors: Zimmermann, G. / Papke, B. / Ismail, S. / Vartak, N. / Chandra, A. / Hoffmann, M. / Hahn, S.A. / Triola, G. / Wittinghofer, A. / Bastiaens, P.I. / Waldmann, H.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,2242
Polymers17,5851
Non-polymers6391
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.910, 55.910, 116.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 17585.121 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-17X / (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate


Mass: 638.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H42N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 18% PEG 4000, 25mM Sodium Acetate, 200mM Ammonium Sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→27.9 Å / Num. all: 8659 / Num. obs: 8659 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.122
Reflection shellResolution: 2.4→2.5 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
RefinementStarting model: 3T5G

3t5g


Resolution: 2.4→27.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.48 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.317 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25659 433 5 %RANDOM
Rwork0.20697 ---
obs0.20949 8225 99.04 %-
all-8225 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.222 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 48 47 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.982.0011668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36323.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10715220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.629159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021924
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 27 -
Rwork0.25 520 -
obs--98.56 %

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