- PDB-7lgi: The haddock model of GDP KRas in complex with promazine using che... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7lgi
Title
The haddock model of GDP KRas in complex with promazine using chemical shift perturbations and intermolecular NOEs
Components
GTPase KRas
Keywords
HYDROLASE / GDP KRAS / SMALL MOLECULE LIGAND / HADDOCK STRUCTURE MODEL / CHEMICAL SHIFT CHANGES / INTERMOLECULAR NOE
Function / homology
Function and homology information
forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / MAPK cascade / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / negative regulation of neuron apoptotic process / Ras protein signal transduction / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family 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
Mass: 284.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
2D 1H-15N HSQC
1
2
1
isotropic
1
3DCBCA(CO)NH
1
3
1
isotropic
1
3D HN(CA)CB
1
4
1
isotropic
1
3DC(CO)NH
1
5
1
isotropic
1
3DH(CCO)NH
2
6
2
isotropic
1
2D 1H-13C HSQC
2
7
2
isotropic
1
3D CCH-TOCSY
2
8
2
isotropic
1
3D 1H-13C NOESY aliphatic
2
9
2
isotropic
1
15N-FILTERED 3D NOESY- 1H
2
10
2
isotropic
1
2D 1H-13C HSQC aliphatic
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Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
1
0.8 mM [U-99% 13C; U-99% 15N] KRAS, 1.0 mM P2Z, 5 mM [U-99% 2H] DTT, 10 uM [U-99% 2H] DSS, 25 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
0.8 mM [U-99% 13C; U-99% 15N] KRAS, 1.0 mM P2Z, 5 mM [U-99% 2H] DTT, 10 uM [U-99% 2H] DSS, 25 mM nature abundance sodium phosphate, 50 mM sodium chloride, 5 mM MAGNESIUM ION, 95% H2O/5% D2O
KRas_P2Z_H2O
90% H2O/10% D2O
solution
2
0.8 mM [U-99% 13C; U-99% 15N] KRAS, 1.0 mM P2Z, 5 mM [U-99% 2H] DTT, 10 uM [U-99% 2H] DSS, 25 mM sodium phosphate, 50 mM sodium chloride, 100% D2O
0.8 mM [U-99% 13C; U-99% 15N] KRas, 1.0 mM P2Z, 5 mM [U-99% 2H] DTT, 10 uM [U-99% 2H] DSS, 25 mM sodium phosphate, 50 mM sodium chloride, 5 mM MAGNESIUM ION, 100% D2O
KRas_P2Z_D2O
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.8mM
KRAS
[U-99% 13C; U-99% 15N]
1
1.0mM
P2Z
naturalabundance
1
5mM
DTT
[U-99% 2H]
1
10uM
DSS
[U-99% 2H]
1
25mM
sodiumphosphate
naturalabundance
1
50mM
sodiumchloride
naturalabundance
1
0.8mM
KRAS
[U-99% 13C; U-99% 15N]
2
1.0mM
P2Z
naturalabundance
2
5mM
DTT
[U-99% 2H]
2
10uM
DSS
[U-99% 2H]
2
25mM
sodiumphosphate
naturalabundance
2
50mM
sodiumchloride
naturalabundance
2
Sample conditions
Conditions-ID
Ionic strength
Label
pH
Pressure (kPa)
Temperature (K)
1
115mM
H2O
7.4
1PAatm
298K
2
115mM
D2O
7.4pD
1PAatm
298K
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NMR measurement
NMR spectrometer
Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
TopSpin
1.3
BrukerBiospin
collection
NMRPipe
2.2
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
NMRViewJ
Johnson, OneMoonScientific
dataanalysis
HADDOCK
A.M.J.J. Bonvin
refinement
Refinement
Method: simulated annealing / Software ordinal: 4
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 10
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