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- PDB-9hmc: Crystal structure of PDE6D in complex with compound 5e -

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Basic information

Entry
Database: PDB / ID: 9hmc
TitleCrystal structure of PDE6D in complex with compound 5e
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / PDE6D / bromoalkane warheads / glutamic acid labelling / targetted covalent inhibitor
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 / cytosol / cytoplasm
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
: / DI(HYDROXYETHYL)ETHER / 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: 1.65 Å
AuthorsZhang, R. / Waldmann, H. / Gasper, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of PDE6D in complex with compound 5e
Authors: Zhang, R.
History
DepositionDec 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0007
Polymers36,5402
Non-polymers1,4605
Water2,648147
1
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0394
Polymers18,2701
Non-polymers7693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9613
Polymers18,2701
Non-polymers6912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.740, 75.650, 82.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18269.879 Da / Num. of mol.: 2
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-A1IWC / 4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxidanylidene-pyrazolo[3,4-d]pyridazin-6-yl]-~{N}-heptyl-~{N}-(piperidin-4-ylmethyl)butane-1-sulfonamide


Mass: 584.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H48N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4 M Na-formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.72 Å / Num. obs: 43331 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 19.66
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.65-1.692.1931690.3672.2761
1.69-1.741.75630530.5061.8261
1.74-1.791.35130130.6621.4071
1.79-1.840.99629220.8111.0381
1.84-1.910.70128030.920.7281
1.91-1.970.5127420.9540.531
1.97-2.050.36726560.9790.3811
2.05-2.130.28425440.9850.2951
2.13-2.220.2224570.9910.2281
2.22-2.330.17923230.9930.1861
2.33-2.460.14622560.9950.1521
2.46-2.610.11621370.9970.1211
2.61-2.790.0919970.9980.0941
2.79-3.010.06718560.9990.0691
3.01-3.30.05117280.9990.0531
3.3-3.690.03915730.9990.041
3.69-4.260.032139410.0341
4.26-5.220.028120110.0291
5.22-7.380.0394710.0321
7.38-46.720.02356010.0241

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.72 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2167 5 %
Rwork0.188 --
obs0.1897 43330 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 101 147 2679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062614
X-RAY DIFFRACTIONf_angle_d0.9143522
X-RAY DIFFRACTIONf_dihedral_angle_d19.1491035
X-RAY DIFFRACTIONf_chiral_restr0.054374
X-RAY DIFFRACTIONf_plane_restr0.008437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.34641420.34742699X-RAY DIFFRACTION100
1.69-1.730.35931420.31282687X-RAY DIFFRACTION100
1.73-1.780.29191430.27332725X-RAY DIFFRACTION100
1.78-1.830.28791430.24662710X-RAY DIFFRACTION100
1.83-1.890.24871420.21992716X-RAY DIFFRACTION100
1.89-1.960.27751430.22662713X-RAY DIFFRACTION100
1.96-2.030.2381430.19252721X-RAY DIFFRACTION100
2.03-2.130.23921440.18622721X-RAY DIFFRACTION100
2.13-2.240.23281440.18682738X-RAY DIFFRACTION100
2.24-2.380.24391430.18432719X-RAY DIFFRACTION100
2.38-2.560.21151450.19522752X-RAY DIFFRACTION100
2.56-2.820.22441440.19822746X-RAY DIFFRACTION100
2.82-3.230.23451460.1992771X-RAY DIFFRACTION100
3.23-4.070.19181480.16292809X-RAY DIFFRACTION100
4.07-46.720.19251550.1572936X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.683 Å / Origin y: 17.6295 Å / Origin z: -15.2848 Å
111213212223313233
T0.168 Å2-0.0028 Å2-0.0053 Å2-0.1874 Å2-0.021 Å2--0.2495 Å2
L0.472 °2-0.0187 °2-0.0214 °2-0.6161 °2-0.462 °2--1.2815 °2
S0.0219 Å °-0.0403 Å °0.1208 Å °-0.0769 Å °0.0005 Å °0.0009 Å °0.0579 Å °0.0076 Å °-0.0201 Å °
Refinement TLS groupSelection details: all

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