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- PDB-7a47: KRASG12C GDP form in complex with Cpd4 -

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Basic information

Entry
Database: PDB / ID: 7a47
TitleKRASG12C GDP form in complex with Cpd4
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / inhibitor / mutant
Function / homologysmall monomeric GTPase / Ca2+ pathway / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE / Chem-QY5 / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBertrand, T. / 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 19, 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3039
Polymers58,1253
Non-polymers3,1796
Water3,801211
1
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4343
Polymers19,3751
Non-polymers1,0602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4343
Polymers19,3751
Non-polymers1,0602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4343
Polymers19,3751
Non-polymers1,0602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.33, 110.33, 116.97
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#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.: 3 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Details: G12C mutant / Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET-28a / Details (production host): T7 promoter / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116-2, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-QY5 / ~{N}-[3-bromanyl-2-(2-methylimidazol-1-yl)pyridin-4-yl]-3-[[3-bromanyl-2-(2-methylimidazol-1-yl)pyridin-4-yl]-propanoyl-amino]propanamide


Mass: 616.308 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H24Br2N8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.1 M Sodium Citrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 2.16→30.73 Å / Num. obs: 44756 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 40.59 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.9
Reflection shellResolution: 2.16→2.22 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3 / Num. unique obs: 3443

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A1X

7a1x


Resolution: 2.16→30.73 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2229 -RANDOM
Rwork0.193 ---
obs-44566 100 %-
Displacement parametersBiso mean: 43.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.524 Å20 Å20 Å2
2--2.524 Å20 Å2
3----5.048 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.16→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 192 211 4405
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014296HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15823HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1551SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes741HARMONIC5
X-RAY DIFFRACTIONt_it4296HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5044SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion19.33
LS refinement shellResolution: 2.16→2.22 Å
RfactorNum. reflection% reflection
Rfree0.242 163 5 %
Rwork0.24 3094 -
obs--100 %

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