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- PDB-6gqx: KRAS-169 Q61H GPPNHP + CH-2 -

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Basic information

Entry
Database: PDB / ID: 6gqx
TitleKRAS-169 Q61H GPPNHP + CH-2
Components(GTPase KRas) x 2
KeywordsONCOPROTEIN / KRAS
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 / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / 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 / G protein activity / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Negative regulation of MAPK pathway / 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 nucleotide triphosphate hydrolases ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F8K / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCruz-Migoni, A. / Quevedo, C.E. / Carr, S.B. / Phillips, S.E.V. / Rabbitts, T.H.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust099246/Z/12/Z United Kingdom
Bloodwise12051 United Kingdom
Medical Research Council (United Kingdom)MR/J000612/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds.
Authors: Cruz-Migoni, A. / Canning, P. / Quevedo, C.E. / Bataille, C.J.R. / Bery, N. / Miller, A. / Russell, A.J. / Phillips, S.E.V. / Carr, S.B. / Rabbitts, T.H.
History
DepositionJun 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
C: GTPase KRas
D: GTPase KRas
E: GTPase KRas
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,24718
Polymers116,9516
Non-polymers4,29712
Water1,71195
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4294
Polymers19,5191
Non-polymers9103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2664
Polymers19,3561
Non-polymers9103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4294
Polymers19,5191
Non-polymers9103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0412
Polymers19,5191
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0412
Polymers19,5191
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0412
Polymers19,5191
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.187, 118.032, 156.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA-2 - 1672 - 171
21PHEPHEBB-2 - 1671 - 170
12TYRTYRAA-3 - 1671 - 171
22TYRTYRCC-3 - 1671 - 171
13PHEPHEAA-2 - 1672 - 171
23PHEPHEDD-2 - 1672 - 171
14PHEPHEAA-2 - 1672 - 171
24PHEPHEEE-2 - 1672 - 171
15TYRTYRAA-3 - 1671 - 171
25TYRTYRFF-3 - 1671 - 171
16PHEPHEBB-2 - 1671 - 170
26PHEPHECC-2 - 1672 - 171
17PHEPHEBB-2 - 1671 - 170
27PHEPHEDD-2 - 1672 - 171
18PHEPHEBB-2 - 1671 - 170
28PHEPHEEE-2 - 1672 - 171
19PHEPHEBB-2 - 1671 - 170
29PHEPHEFF-2 - 1672 - 171
110PHEPHECC-2 - 1672 - 171
210PHEPHEDD-2 - 1672 - 171
111PHEPHECC-2 - 1672 - 171
211PHEPHEEE-2 - 1672 - 171
112TYRTYRCC-3 - 1671 - 171
212TYRTYRFF-3 - 1671 - 171
113PHEPHEDD-2 - 1672 - 171
213PHEPHEEE-2 - 1672 - 171
114PHEPHEDD-2 - 1672 - 171
214PHEPHEFF-2 - 1672 - 171
115PHEPHEEE-2 - 1672 - 171
215PHEPHEFF-2 - 1672 - 171

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 2 types, 6 molecules ACDEFB

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


Mass: 19519.014 Da / Num. of mol.: 5 / Mutation: Q61H
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
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19355.840 Da / Num. of mol.: 1 / Mutation: Q61H
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

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Non-polymers , 4 types, 107 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-F8K / [4-[[2-methoxy-4-(3-methoxyphenyl)phenyl]amino]phenyl]methyl-dimethyl-azanium


Mass: 363.473 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8-15% w/v polyethylene glycol 3350 and 0.2 M Lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→156 Å / Num. obs: 60229 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Rrim(I) all: 0.108 / Net I/av σ(I): 15.6 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4369 / CC1/2: 0.908 / Rpim(I) all: 0.43 / Rrim(I) all: 0.939 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFT

3gft


Resolution: 2.2→94.21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.86 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23026 3016 5 %RANDOM
Rwork0.20161 ---
obs0.20302 57101 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.235 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--3.24 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→94.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7779 0 276 95 8150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0158243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177295
X-RAY DIFFRACTIONr_angle_refined_deg1.451.73611155
X-RAY DIFFRACTIONr_angle_other_deg0.4811.72417079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93118.693306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.173151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0681559
X-RAY DIFFRACTIONr_chiral_restr0.0620.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021494
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7073.8053937
X-RAY DIFFRACTIONr_mcbond_other3.7063.8063938
X-RAY DIFFRACTIONr_mcangle_it5.4595.6694900
X-RAY DIFFRACTIONr_mcangle_other5.4595.674901
X-RAY DIFFRACTIONr_scbond_it5.2684.5284306
X-RAY DIFFRACTIONr_scbond_other5.2694.5284304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2796.5196253
X-RAY DIFFRACTIONr_long_range_B_refined9.9446.218612
X-RAY DIFFRACTIONr_long_range_B_other9.93946.2078610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53870.07
12B53870.07
21A53340.07
22C53340.07
31A50570.07
32D50570.07
41A50170.08
42E50170.08
51A50890.08
52F50890.08
61B52670.08
62C52670.08
71B50450.07
72D50450.07
81B50000.08
82E50000.08
91B50730.07
92F50730.07
101C49850.08
102D49850.08
111C49890.08
112E49890.08
121C50440.08
122F50440.08
131D50570.07
132E50570.07
141D50920.07
142F50920.07
151E50410.08
152F50410.08
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 233 -
Rwork0.324 4096 -
obs--98.95 %

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