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- PDB-9glu: Crystal structure of KRasG12D-GDP in complex with the peptide MPB1 -

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Basic information

Entry
Database: PDB / ID: 9glu
TitleCrystal structure of KRasG12D-GDP in complex with the peptide MPB1
Components
  • Isoform 2B of GTPase KRas
  • Peptide MPB1
KeywordsHYDROLASE / GTPASE / SIGNALING PROTEIN / SMALL G-PROTEIN
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / positive regulation of Rac protein signal transduction / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / 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 / glial cell proliferation / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / 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 / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / RAF activation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 KD Mutants / visual learning / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / RAS processing / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOstermann, N. / Zink, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Identification and characterization of binders to a cryptic and functional pocket in KRAS.
Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, ...Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, F. / Ostermann, N. / Jahnke, W. / Dumelin, C.E. / Leder, L. / Esser, O. / Muller, L. / Marzinzik, A. / Cebe, R. / Muller, K. / Galli, G.G. / Tordella, L. / Cotesta, S. / Brachmann, S.M. / Maira, S.M.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 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: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Peptide MPB1
D: Peptide MPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9698
Polymers42,0344
Non-polymers9354
Water6,666370
1
A: Isoform 2B of GTPase KRas
C: Peptide MPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4844
Polymers21,0172
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-28 kcal/mol
Surface area8660 Å2
MethodPISA
2
B: Isoform 2B of GTPase KRas
D: Peptide MPB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4844
Polymers21,0172
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.407, 79.44, 128.529
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19364.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase
#2: Protein/peptide Peptide MPB1


Mass: 1652.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 370 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 0.1 mM BisTris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.9→64.26 Å / Num. obs: 34233 / % possible obs: 99.8 % / Redundancy: 6.45 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.57
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.59 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 685 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VTYV

Resolution: 1.9→49.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1712 -RANDOM
Rwork0.1836 ---
obs0.1851 34233 99.8 %-
Displacement parametersBiso mean: 30.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.2008 Å20 Å20 Å2
2---1.0544 Å20 Å2
3---0.8535 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 294 370 3371
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083079HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14169HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1093SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes537HARMONIC5
X-RAY DIFFRACTIONt_it3079HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3074SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion15.81
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.2937 34 -
Rwork0.2665 --
obs0.2679 685 100 %
Refinement TLS params.

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)
10.6595-0.1767-0.11990.42840.11630.9509-0.00410.0140.01790.014-0.0199-0.0050.0179-0.0050.024-0.0049-0.00330.0027-0.0366-0.0138-0.0146-21.7219.9148-12.0425
20.7827-0.1540.06351.60360.27893.16770.0485-0.13340.0853-0.13340.0254-0.02810.0853-0.0281-0.0738-0.0312-0.0129-0.0102-0.0410.0115-0.0655-23.8412-10.57516.0722
30.05920.08370.10280.8678-1.27092.51460.0036-0.10750.1713-0.1075-0.05760.12730.17130.12730.054-0.04020.02310.0202-0.0548-0.0127-0.0217-18.4192-5.334610.8062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 169
2X-RAY DIFFRACTION1{ A|* }A1001
3X-RAY DIFFRACTION2{ B|* }B1 - 168
4X-RAY DIFFRACTION2{ B|* }B1001
5X-RAY DIFFRACTION3{ C|* }C1 - 14
6X-RAY DIFFRACTION3{ D|* }D1 - 14

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