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- PDB-7q9s: Crystal structure of PDE6D KRas peptide complex with Compound-1 -

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Basic information

Entry
Database: PDB / ID: 7q9s
TitleCrystal structure of PDE6D KRas peptide complex with Compound-1
Components
  • KRas
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsPROTEIN BINDING / Complex / Inhibitor
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 / 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
Chem-9TI / FARNESYL / 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: 1.85 Å
AuthorsYelland, T. / Ismail, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.
Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. ...Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. / Jamieson, A. / Chen, Y.X. / McArthur, D. / Bower, J. / Ismail, S.
History
DepositionNov 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
CCC: KRas
DDD: KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,35817
Polymers37,9404
Non-polymers1,41813
Water4,017223
1
BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
DDD: KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7199
Polymers18,9702
Non-polymers7497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
CCC: KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6398
Polymers18,9702
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.104, 81.123, 118.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11BBB-377-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules BBBAAACCCDDD

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


Mass: 17440.990 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: Protein/peptide KRas /


Mass: 1528.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 236 molecules

#3: Chemical ChemComp-9TI / 2-methyl-3-(1~{H}-pyrazol-5-yl)imidazo[1,2-a]pyridine


Mass: 198.224 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H10N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H26
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulphate, 0.1M Tris pH 8.5 and 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.85→40.657 Å / Num. obs: 32070 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.999 / Net I/σ(I): 8.4
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 2320 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TB5

5tb5


Resolution: 1.85→40.657 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.342 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2273 1575 4.917 %
Rwork0.1993 30459 -
all0.201 --
obs-32034 99.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.262 Å2
Baniso -1Baniso -2Baniso -3
1-0.019 Å20 Å20 Å2
2---0.226 Å20 Å2
3---0.207 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 113 223 2825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132804
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172649
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.6733773
X-RAY DIFFRACTIONr_angle_other_deg1.4341.5996137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83322.105152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2711518
X-RAY DIFFRACTIONr_chiral_restr0.0540.2346
X-RAY DIFFRACTIONr_chiral_restr_other0.0060.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023133
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
X-RAY DIFFRACTIONr_nbd_refined0.4980.2506
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2970.22547
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21244
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.21312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3060.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3880.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.216
X-RAY DIFFRACTIONr_nbd_other0.2890.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.211
X-RAY DIFFRACTIONr_mcbond_it2.8932.4341319
X-RAY DIFFRACTIONr_mcbond_other2.8922.4341320
X-RAY DIFFRACTIONr_mcangle_it3.8253.6141662
X-RAY DIFFRACTIONr_mcangle_other3.8243.6141663
X-RAY DIFFRACTIONr_scbond_it4.3193.0011484
X-RAY DIFFRACTIONr_scbond_other4.3183.0021485
X-RAY DIFFRACTIONr_scangle_it6.5614.2372111
X-RAY DIFFRACTIONr_scangle_other6.564.2392112
X-RAY DIFFRACTIONr_lrange_it8.7929.0943081
X-RAY DIFFRACTIONr_lrange_other8.78929.1073082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.2851160.25121770.25223150.8770.88799.04970.227
1.898-1.950.26990.23921860.2422860.8720.89999.95630.213
1.95-2.0060.217990.21421260.21422260.9170.9399.95510.189
2.006-2.0680.2541010.20320610.20621630.9180.93699.95380.185
2.068-2.1360.251090.20419660.20720750.9080.9341000.18
2.136-2.210.2241170.21219060.21320230.9340.9311000.19
2.21-2.2940.251940.20518610.20819550.9160.931000.186
2.294-2.3870.236900.20817960.20918860.9250.9371000.186
2.387-2.4930.257950.21117170.21418130.9080.92399.94480.194
2.493-2.6140.272710.20516660.20817370.9060.9321000.187
2.614-2.7550.226710.20515830.20616540.9380.9381000.186
2.755-2.9210.232800.20314880.20415680.9310.9431000.19
2.921-3.1210.264610.21614340.21814950.920.9291000.205
3.121-3.370.246700.212920.20213620.9320.9421000.195
3.37-3.6890.211760.18812130.18912890.9460.9551000.188
3.689-4.120.163600.16310900.16311500.9720.9711000.165
4.12-4.7490.163500.1539830.15410340.9690.9799.90330.157
4.749-5.7970.231510.1818430.1848940.9520.9631000.19
5.797-8.1160.257380.2626690.2617070.9340.9331000.262
8.116-40.6570.247270.2264010.2274280.9470.9521000.229
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.110.2290.11310.47920.25540.615-0.00920.00520.0243-0.01050.01090.04570.04850.0327-0.00160.044-0.0276-0.0070.0614-0.02860.0328-3.7245-16.49923.2144
20.28350.15080.0410.6483-0.31010.2886-0.02830.0293-0.04670.02290.0135-0.0755-0.04570.01610.01480.0191-0.0059-0.01250.05080.00790.0408-15.2148-36.8674-26.2495
31.8602-1.5799-1.77211.34261.50471.68830.06680.11-0.0784-0.0805-0.120.0699-0.0812-0.10140.05330.05990.0371-0.04620.0667-0.00390.0507-18.7045-51.563-20.7566
40.38211.04182.03920.3734-1.57513.79490.07940.0627-0.0715-0.42230.2475-0.39120.73110.3222-0.32690.04460.0095-0.00760.0594-0.05260.048310.2174-19.06349.5069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLBBB2 - 150
2X-RAY DIFFRACTION2ALLAAA1 - 150
3X-RAY DIFFRACTION3ALLCCC19 - 23
4X-RAY DIFFRACTION4ALLDDD1 - 4

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