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- PDB-4jv6: The crystal structure of PDE6D in complex to inhibitor-1 -

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Basic information

Entry
Database: PDB / ID: 4jv6
TitleThe crystal structure of PDE6D in complex to inhibitor-1
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 / Protein binding-inhibitor complex
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
1-benzyl-2-phenyl-1H-benzimidazole / 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: 1.87 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 1.2Sep 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)18,1543
Polymers17,5851
Non-polymers5692
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.360, 55.360, 115.560
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
11B-311-

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: 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-18F / 1-benzyl-2-phenyl-1H-benzimidazole


Mass: 284.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM Sodium Acetate, 2.0M NaCl, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2011
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.87→27.68 Å / Num. all: 17518 / Num. obs: 17518 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.87→1.9 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
PRODCdata collection
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 1.87→27.68 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.796 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22739 876 5 %RANDOM
Rwork0.1751 ---
obs0.17779 16641 99.45 %-
all-16641 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.611 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.9 Å20 Å2
2--1.81 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 44 157 1393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.991726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.31923.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43415230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.677159
X-RAY DIFFRACTIONr_chiral_restr0.1890.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02965
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: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 54 -
Rwork0.217 1087 -
obs--98.79 %

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