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- PDB-8qe7: NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 2-(met... -

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Basic information

Entry
Database: PDB / ID: 8qe7
TitleNMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 2-(methylsulfonylmethyl)-1H-benzimidazole
ComponentsRASK GTPase (Fragment)
KeywordsONCOPROTEIN / Complex / Fragment
Function / homology
Function and homology information


small monomeric GTPase / GTPase activity / GTP binding / signal transduction / membrane
Similarity search - Function
Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / 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
2-[(methylsulfonyl)methyl]-1H-benzimidazole / small monomeric GTPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBuetikofer, M. / Orts, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss Cancer LeagueKFS-4903-08-2019 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: NMR2-Based Drug Discovery Pipeline Presented on the Oncogenic Protein KRAS.
Authors: Butikofer, M. / Torres, F. / Kadavath, H. / Gamperli, N. / Abi Saad, M.J. / Zindel, D. / Coudevylle, N. / Riek, R. / Orts, J.
History
DepositionAug 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RASK GTPase (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5082
Polymers19,2981
Non-polymers2101
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RASK GTPase (Fragment)


Mass: 19297.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KRAS G12V GMPPNP bound / Source: (gene. exp.) Homo sapiens (human) / Gene: Kras / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L2RV33
#2: Chemical ChemComp-T6J / 2-[(methylsulfonyl)methyl]-1H-benzimidazole


Mass: 210.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM KRAS G12V GMPPNP, 5 mM 2-(methylsulfonylmethyl)-1H-benzimidazole, 100% D2O
Details: KRAS G12V GMPPNP / Label: Unlabelled / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKRAS G12V GMPPNPnatural abundance1
5 mM2-(methylsulfonylmethyl)-1H-benzimidazolenatural abundance1
Sample conditionsDetails: 25 mM Tris, 100 mM NaCl, 5 mM MgCl2, 5mM BME all deuterated in D2O
Ionic strength: 130 mM / Label: conditions1 / pH: 7.4 pD / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4 / Conformers submitted total number: 4

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