- PDB-3kkm: Crystal structure of H-Ras T35S in complex with GppNHp -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3kkm
Title
Crystal structure of H-Ras T35S in complex with GppNHp
Components
GTPase HRas
Keywords
SIGNALING PROTEIN / GTP-binding / GTPase
Function / homology
Function and homology information
GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / 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 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / endocytosis / Negative regulation of MAPK pathway / RAS processing / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / insulin receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.7→23.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.818 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23228
1109
5.1 %
RANDOM
Rwork
0.19473
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-
-
all
0.19655
20512
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obs
0.19655
20512
99.98 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 19.911 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→23.72 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1224
0
43
108
1375
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
1289
X-RAY DIFFRACTION
r_angle_refined_deg
1.388
1.999
1750
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.681
5
155
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.914
24.355
62
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.652
15
224
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.174
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
196
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
955
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.2
602
X-RAY DIFFRACTION
r_nbtor_refined
0.31
0.2
878
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.161
0.2
107
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.202
0.2
37
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.207
0.2
19
X-RAY DIFFRACTION
r_mcbond_it
0.979
1.5
794
X-RAY DIFFRACTION
r_mcangle_it
1.545
2
1249
X-RAY DIFFRACTION
r_scbond_it
2.279
3
560
X-RAY DIFFRACTION
r_scangle_it
3.587
4.5
501
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.321
81
-
Rwork
0.233
1498
-
obs
-
1498
100 %
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