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- PDB-12uw: Crystal structure of KRAS(Q61K) bound to GDP and ligand -

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Basic information

Entry
Database: PDB / ID: 12uw
TitleCrystal structure of KRAS(Q61K) bound to GDP and ligand
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / KRAS / GTPase / GDP-bound
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / LRR domain binding / response to isolation stress / response to gravity / myoblast proliferation / cardiac muscle cell proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells ...response to mineralocorticoid / GMP binding / LRR domain binding / response to isolation stress / response to gravity / myoblast proliferation / cardiac muscle cell proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of Ras protein signal transduction / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / liver development / GRB2 events in ERBB2 signaling / Downstream signal transduction / response to glucocorticoid / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / female pregnancy / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by SCF-KIT / RAF activation / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / cytokine-mediated signaling pathway / cytoplasmic side of plasma membrane / Signaling by RAF1 mutants / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Negative regulation of MAPK pathway / RAS processing / Regulation of RAS by GAPs / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence / GDP binding / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade / G protein activity / Ca2+ pathway / Ras protein signal transduction / mitochondrial outer membrane / Golgi membrane / focal adhesion / positive regulation of gene expression / positive regulation of cell population proliferation / GTPase activity / endoplasmic reticulum membrane / GTP binding / protein-containing complex binding
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWang, Y.-C. / Zhang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
Damon Runyon Cancer Research Foundation United States
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Bronsted-basic small molecules activate GTP hydrolysis in KRAS-Q61 mutants.
Authors: Wang, Y.C. / Chen, S.C. / Cao, Y. / Wu, Y. / Shi, Z. / Wang, C.D. / Norinskiy, M.A. / Celik, H. / Zhang, Z.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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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
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9848
Polymers38,6602
Non-polymers2,3256
Water3,495194
1
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4924
Polymers19,3301
Non-polymers1,1623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4924
Polymers19,3301
Non-polymers1,1623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.492, 37.765, 71.700
Angle α, β, γ (deg.)90.000, 94.802, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 19329.861 Da / Num. of mol.: 2 / Mutation: Q61K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116, small monomeric GTPase
#2: Chemical ChemComp-A1DEM / (4P)-5-ethynyl-6-fluoro-4-(8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-4-{(1R,5S)-8-[(1-methyl-1H-imidazol-4-yl)methyl]-3,8-diazabicyclo[3.2.1]octan-3-yl}pyrido[4,3-d]pyrimidin-7-yl)naphthalen-2-ol


Mass: 694.748 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H37F3N8O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 41.01 % / Description: Thin plate-shaped crystals.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M LiCl, 0.1 M HEPES pH 7.5, and 32% PEG 6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2026
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→47.75 Å / Num. obs: 20292 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Χ2: 1.01 / Net I/σ(I): 15
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1590 / CC1/2: 0.855 / Rpim(I) all: 0.433 / Rrim(I) all: 0.822 / Χ2: 0.86 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIX2.0_5936phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.75 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7565
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 2004 9.88 %
Rwork0.2014 18274 -
obs0.2061 20278 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.42 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 160 194 2892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252776
X-RAY DIFFRACTIONf_angle_d0.75893791
X-RAY DIFFRACTIONf_chiral_restr0.0436416
X-RAY DIFFRACTIONf_plane_restr0.0035469
X-RAY DIFFRACTIONf_dihedral_angle_d20.81931008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.34391370.28091318X-RAY DIFFRACTION99.39
2.1-2.160.32481430.2621283X-RAY DIFFRACTION99.3
2.16-2.220.30271420.25251294X-RAY DIFFRACTION99.03
2.22-2.290.30011490.23991268X-RAY DIFFRACTION99.37
2.29-2.380.31231380.24481295X-RAY DIFFRACTION98.76
2.38-2.470.29441440.23771283X-RAY DIFFRACTION98.96
2.47-2.580.30461350.22861295X-RAY DIFFRACTION100
2.58-2.720.27891490.23731317X-RAY DIFFRACTION100
2.72-2.890.30521390.24161310X-RAY DIFFRACTION100
2.89-3.110.29741490.22221294X-RAY DIFFRACTION99.18
3.11-3.430.27231490.19771311X-RAY DIFFRACTION99.05
3.43-3.920.21431390.17711297X-RAY DIFFRACTION99.03
3.92-4.940.17091410.15281336X-RAY DIFFRACTION99.93
4.94-47.750.20521500.17491373X-RAY DIFFRACTION98.96
Refinement TLS params.Method: refined / Origin x: -1.9004201931884 Å / Origin y: 9.5568838014576 Å / Origin z: 17.611145699247 Å
111213212223313233
T0.25017267226857 Å20.015268425854819 Å20.017538191754054 Å2-0.19947815430275 Å20.03538994229471 Å2--0.25136757357044 Å2
L3.3600923966779 °21.0688116112002 °21.8223725555913 °2-0.43455238922979 °20.61510394079155 °2--1.4109771386858 °2
S-0.054379055871765 Å °0.25944605085759 Å °0.19458452920199 Å °-0.058165748824403 Å °-0.011208224874855 Å °-0.0053641704399941 Å °-0.079316559337205 Å °0.13969121496998 Å °0.06143731642261 Å °
Refinement TLS groupSelection details: all

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