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- PDB-7a1w: KRASG12C GDP form in complex with Cpd3 -

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Basic information

Entry
Database: PDB / ID: 7a1w
TitleKRASG12C GDP form in complex with Cpd3
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / inhibitor / mutant
Function / homologysmall monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Chem-QWK / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMathieu, M. / Steier, V.
CitationJournal: Small Gtpases / Year: 2022
Title: KRAS G12C fragment screening renders new binding pockets.
Authors: Mathieu, M. / Steier, V. / Fassy, F. / Delorme, C. / Papin, D. / Genet, B. / Duffieux, F. / Bertrand, T. / Delarbre, L. / Le-Borgne, H. / Parent, A. / Didier, P. / Marquette, J.P. / ...Authors: Mathieu, M. / Steier, V. / Fassy, F. / Delorme, C. / Papin, D. / Genet, B. / Duffieux, F. / Bertrand, T. / Delarbre, L. / Le-Borgne, H. / Parent, A. / Didier, P. / Marquette, J.P. / Lowinski, M. / Houtmann, J. / Lamberton, A. / Debussche, L. / Alexey, R.
History
DepositionAug 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5306
Polymers19,3751
Non-polymers1,1555
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-27 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.55, 38.55, 186.07
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19374.902 Da / Num. of mol.: 1 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET-28a / Details (production host): T7 promoter / Cell (production host): NA / Organ (production host): NA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): NA / Tissue (production host): NA / Variant (production host): NA / References: UniProt: P01116-2, small monomeric GTPase

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-QWK / ~{N}-[6-(phenylmethyl)-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-2-yl]propanamide / RA303


Mass: 296.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350 20% - Na2HPO4 200mM - pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.76→46.52 Å / Num. obs: 16891 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1138 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal model

Resolution: 1.76→33.39 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 840 5 %RANDOM
Rwork0.2001 ---
obs-16786 99.73 %-
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.9267 Å20 Å20 Å2
2--2.9267 Å20 Å2
3----5.8534 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.76→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 78 111 1514
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011442HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.971951HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d525SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes216HARMONIC5
X-RAY DIFFRACTIONt_it1442HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion184SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1793SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion16.87
LS refinement shellResolution: 1.76→1.88 Å
RfactorNum. reflection% reflection
Rfree0.3681 146 5 %
Rwork0.2617 2775 -
obs--99.7 %

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