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Yorodumi- PDB-8qdk: NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with N-(fur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qdk | ||||||
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Title | NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with N-(furan-2-ylmethyl)-1H-benzimidazol-2-amine | ||||||
Components | RASK GTPase (Fragment) | ||||||
Keywords | ONCOPROTEIN / Complex / Fragment | ||||||
Function / homology | Function and homology information small monomeric GTPase / GDP binding / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Buetikofer, M. / Orts, J. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 5-(1H-indol-2-l)piperazin-2-one Authors: Buetikofer, M. / Orts, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qdk.cif.gz | 223.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qdk.ent.gz | 177.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qdk_validation.pdf.gz | 476 KB | Display | wwPDB validaton report |
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Full document | 8qdk_full_validation.pdf.gz | 496 KB | Display | |
Data in XML | 8qdk_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 8qdk_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/8qdk ftp://data.pdbj.org/pub/pdb/validation_reports/qd/8qdk | HTTPS FTP |
-Related structure data
Related structure data | 8pi0C 8piyC 8qdpC 8qdsC 8qdtC 8qdwC 8qe7C 8qeiC 8qejC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19297.773 Da / Num. of mol.: 1 / Mutation: G12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Kras / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L2RV33 |
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#2: Chemical | ChemComp-WZD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 5 mM N-(furan-2-ylmethyl)-1H-benzimidazol-2-amine,, 1 mM [U-100% 13C; U-100% 15N] K-Ras G12V (GMPPNP bound), 100% D2O Label: 13C, 15N / Solvent system: 100% D2O | ||||||||||||
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Sample |
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Sample conditions | Details: 25 mM Tris (deut), 100 mM NaCl, 5 mM MgCl2, 5 mM BME (deut) Ionic strength: 130 mM / Label: condition_1 / pH: 7.4 pD / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 4 / Conformers submitted total number: 4 |