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- PDB-36oi: Tri-complex of Compound 1, KRAS G13C, and CypA -

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Basic information

Entry
Database: PDB / ID: 36oi
TitleTri-complex of Compound 1, KRAS G13C, and CypA
Components
  • Isoform 2B of GTPase KRas
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsSIGNALING PROTEIN / inhibitor / complex / small GTPase / cancer / tri-complex / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / activation of protein kinase B activity / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / Early Phase of HIV Life Cycle / regulation of synaptic transmission, GABAergic / Integration of provirus / negative regulation of epithelial cell differentiation / response to isolation stress / APOBEC3G mediated resistance to HIV-1 infection / negative regulation of protein phosphorylation / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / myoblast proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / viral release from host cell / RAS signaling downstream of NF1 loss-of-function variants / Binding and entry of HIV virion / Calcineurin activates NFAT / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / skeletal muscle cell differentiation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / cardiac muscle cell proliferation / SHC1 events in ERBB4 signaling / Signalling to RAS / negative regulation of protein kinase activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / positive regulation of viral genome replication / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / glial cell proliferation / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / neutrophil chemotaxis / striated muscle cell differentiation / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / response to glucocorticoid / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Ras activation upon Ca2+ influx through NMDA receptor / :
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain 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
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRead, B. / Tomlinson, A.C.A. / Knox, J.E. / Yano, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Discov / Year: 2026
Title: Selective Inhibition of KRASG13C Reveals an Increased Dependence on Wild-Type RAS Isoforms in Codon 13 RAS-Mutant Cancers.
Authors: Seamon, K.J. / Zhuang, Y. / Yang, Y.C. / Chakraborty, S. / Cregg, J. / Tomlinson, A.C.A. / Gould, A. / Ahler, E. / Maldonato, B.J. / Spradlin, J.N. / Pota, K. / Weller, C. / Marquez, A. / ...Authors: Seamon, K.J. / Zhuang, Y. / Yang, Y.C. / Chakraborty, S. / Cregg, J. / Tomlinson, A.C.A. / Gould, A. / Ahler, E. / Maldonato, B.J. / Spradlin, J.N. / Pota, K. / Weller, C. / Marquez, A. / Wang, Z. / Koltun, E.S. / Knox, J.E. / Gill, A.L. / Smith, J.A.M. / Singh, M. / Jiang, J. / Wildes, D. / Holderfield, M.
History
DepositionJun 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,96210
Polymers75,0574
Non-polymers2,9056
Water12,160675
1
A: Isoform 2B of GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9815
Polymers37,5292
Non-polymers1,4533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9815
Polymers37,5292
Non-polymers1,4533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.050, 105.080, 66.090
Angle α, β, γ (deg.)90.000, 90.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 19404.928 Da / Num. of mol.: 2
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, small monomeric GTPase
#2: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18123.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase

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Non-polymers , 4 types, 681 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1AOL / (3R)-N-[(2S)-1-{[(1M,8R,10R,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name)


Mass: 906.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H67N7O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.47→36.7 Å / Num. obs: 109128 / % possible obs: 98.19 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.047 / Net I/σ(I): 7.43
Reflection shellResolution: 1.47→1.49 Å / Rmerge(I) obs: 1.967 / Mean I/σ(I) obs: 0.63 / Num. unique obs: 3609 / CC1/2: 0.302 / Rpim(I) all: 1.128

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→36.7 Å / SU ML: 0.2304 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 5401 4.95 %
Rwork0.1917 103701 -
obs0.1939 109102 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.32 Å2
Refinement stepCycle: LAST / Resolution: 1.47→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 196 675 6113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945604
X-RAY DIFFRACTIONf_angle_d1.10157585
X-RAY DIFFRACTIONf_chiral_restr0.0921809
X-RAY DIFFRACTIONf_plane_restr0.0085981
X-RAY DIFFRACTIONf_dihedral_angle_d13.54722203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.3821530.35033440X-RAY DIFFRACTION98.63
1.49-1.50.33881700.30573543X-RAY DIFFRACTION98.83
1.5-1.520.32891800.30253429X-RAY DIFFRACTION98.96
1.52-1.540.35071900.29483488X-RAY DIFFRACTION99.3
1.54-1.560.34472110.28543482X-RAY DIFFRACTION99.49
1.56-1.580.34451840.28063443X-RAY DIFFRACTION99.42
1.58-1.610.29181640.26573548X-RAY DIFFRACTION99.44
1.61-1.630.29831850.25393433X-RAY DIFFRACTION99.26
1.63-1.660.29551830.23293546X-RAY DIFFRACTION99.07
1.66-1.680.30881490.23683455X-RAY DIFFRACTION98.71
1.68-1.710.28532110.22663429X-RAY DIFFRACTION98.62
1.71-1.740.27912010.22163406X-RAY DIFFRACTION98.12
1.74-1.780.27181760.21013476X-RAY DIFFRACTION97.36
1.78-1.810.23872000.18913433X-RAY DIFFRACTION99.32
1.81-1.850.25091790.18913511X-RAY DIFFRACTION99.51
1.85-1.90.27771960.20423495X-RAY DIFFRACTION99.43
1.9-1.940.43311650.35093122X-RAY DIFFRACTION88.98
1.94-20.25691920.2123509X-RAY DIFFRACTION99.22
2-2.050.26342020.18983432X-RAY DIFFRACTION99.13
2.05-2.120.23261980.18743462X-RAY DIFFRACTION99.16
2.12-2.20.24251990.19143478X-RAY DIFFRACTION98.84
2.2-2.280.33931450.28353216X-RAY DIFFRACTION90.4
2.28-2.390.23951870.19743457X-RAY DIFFRACTION98.57
2.39-2.510.24441590.18763495X-RAY DIFFRACTION98.62
2.51-2.670.22561850.17783487X-RAY DIFFRACTION98.58
2.67-2.880.22421540.18173508X-RAY DIFFRACTION99.08
2.88-3.170.23361610.17833415X-RAY DIFFRACTION96.03
3.17-3.620.18671640.163457X-RAY DIFFRACTION97.47
3.62-4.560.17991810.13813529X-RAY DIFFRACTION99.2
4.57-36.70.16471770.14553577X-RAY DIFFRACTION99.15
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04085164356-0.2522163785580.377216192431.388470980760.2156716205871.267008058050.03509719422620.0579441759783-0.0775501992413-0.03501079293340.03589547327580.01339763405430.06134629156660.0668419325178-0.07026558793050.1653758520210.00262157873187-0.01332172675850.2458729158840.003162663283160.1723115522984.6432627979612.32663567014.92170557184
21.191695137380.137734839182-0.5784237251551.02277915109-0.07129667797111.320439660380.0981795833179-0.1041878937780.09663640840120.1019955008220.04709610988330.0666252015167-0.1965134547810.0532934365317-0.1430620685660.205090524669-0.01449780718610.0266374071030.2515889158610.00491602578580.1775087878524.1071377070530.748959787132.10049659
31.34015387854-0.087025497383-0.313929924561.57134899982-0.1831589580651.458697934820.0376364729734-0.05731716823370.120007888405-0.0588582463601-0.01960638637390.0593319637046-0.123710034234-0.0134015439416-0.01670994142660.1500052222080.01071669208640.004847780930020.181158134027-0.01784783696910.156734143248-18.0000874236.0674605374-1.41666519977
41.39133776540.1306976882530.4612383208371.28369076363-0.1827502916071.193956447060.00614483496140.111005726541-0.1112050917880.02388829634490.02454687046760.05513526455170.03524496549550.0116437509459-0.02618481703860.1199375403870.001554863088340.003957333697060.201556963932-0.002866919940090.136446724733-18.6768511856.7347674118137.5974256413
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 0 through 169)AA0 - 1691 - 170
22(chain 'B' and resid 0 through 169)BD0 - 1691 - 170
33(chain 'C' and resid 2 through 201)CG - H2 - 2011
44(chain 'D' and resid 1 through 201)DI - J1 - 2011

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