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- PDB-7mdp: KRas G12C in complex with G-2897 -

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Basic information

Entry
Database: PDB / ID: 7mdp
TitleKRas G12C in complex with G-2897
Components
  • IgG heavy chain
  • IgG light chain
  • Isoform 2B of GTPase KRas
KeywordsHYDROLASE/Immune System / KRAS / GTPase / HYDROLASE / HYDROLASE-Immune System complex
Function / homology
Function and homology information


small monomeric GTPase / Ca2+ pathway
Similarity search - Function
P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLIC ACID / GUANOSINE-5'-DIPHOSPHATE / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 4-(trifluoromethyl)-1,3-benzothiazol-2-amine / Isoform 2B of GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsOh, A. / Frank, Y. / Wang, W.
CitationJournal: Nat.Biotechnol. / Year: 2022
Title: Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors.
Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, ...Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, Y. / Merchant, M. / Koeppen, H. / Quinn, J.G. / Malhotra, S. / Do, S. / Gazzard, L. / Purkey, H.E. / Rudolph, J. / Mulvihill, M.M. / Koerber, J.T. / Wang, W. / Evangelista, M.
History
DepositionApr 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
H: IgG heavy chain
I: IgG light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,89721
Polymers66,0303
Non-polymers2,86818
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.365, 68.919, 100.543
Angle α, β, γ (deg.)90.000, 114.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21H-426-

HOH

31I-468-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19317.850 Da / Num. of mol.: 1 / Mutation: G12C
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, small monomeric GTPase

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Antibody , 2 types, 2 molecules HI

#2: Antibody IgG heavy chain


Mass: 23833.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody IgG light chain


Mass: 22878.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 9 types, 161 molecules

#4: Chemical ChemComp-Z07 / 4-(trifluoromethyl)-1,3-benzothiazol-2-amine


Mass: 218.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3N2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7AsO2
#9: Chemical
ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H28O7
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 21 % PEG 4K and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→37.902 Å / Num. obs: 75922 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Net I/σ(I): 10.2
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.64 / Num. measured all: 28439 / Num. unique obs: 8279 / CC1/2: 0.4 / Rpim(I) all: 1.043 / Rrim(I) all: 1.95 / Net I/σ(I) obs: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.12-2829_finalrefinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC8

6xc8
PDB Unreleased entry


Resolution: 1.96→37.902 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 33.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 3833 5.05 %
Rwork0.1948 72089 -
obs0.1966 75922 57.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.64 Å2 / Biso mean: 57.5263 Å2 / Biso min: 19.95 Å2
Refinement stepCycle: final / Resolution: 1.96→37.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 138 143 4860
Biso mean--86.75 45.13 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064823
X-RAY DIFFRACTIONf_angle_d0.8496539
X-RAY DIFFRACTIONf_chiral_restr0.051726
X-RAY DIFFRACTIONf_plane_restr0.01822
X-RAY DIFFRACTIONf_dihedral_angle_d16.9332861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9604-1.98520.382680.3758962
1.9852-2.01140.5680.33622916
2.0114-2.03890.3474240.332945610
2.0389-2.0680.2513290.311161313
2.068-2.09890.2984440.328392120
2.0989-2.13170.2542440.3222109124
2.1317-2.16660.3262670.3055133529
2.1666-2.2040.2902760.2948140231
2.204-2.24410.35281120.3321160535
2.2441-2.28720.40571080.3402190441
2.2872-2.33390.35771050.3048205445
2.3339-2.38460.3021130.2872230850
2.3846-2.44010.32091260.2817260256
2.4401-2.50110.27511170.2866279060
2.5011-2.56870.28521740.281298165
2.5687-2.64430.28512070.2803330273
2.6443-2.72960.28562040.2825364180
2.7296-2.82720.28582160.2726404287
2.8272-2.94030.26252440.2487429794
2.9403-3.07410.3212290.2463440696
3.0741-3.23610.2872550.2307442896
3.2361-3.43870.25832460.2089423192
3.4387-3.7040.23022120.1819422392
3.704-4.07630.19671970.1537424492
4.0763-4.66530.14862430.1231429194
4.6653-5.87420.16592240.1293430993
5.8742-37.9020.1692010.1455422691
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)
11.4310.2057-0.05110.7960.15931.66940.0057-0.5735-0.09270.1493-0.019-0.40620.49890.92410.00090.90880.13050.01441.25810.05740.3434-4.62438.69546.948
21.87460.00180.12111.7992-0.07831.07440.0757-0.4804-0.33080.34040.1192-0.00330.03390.02850.00680.2040.02650.00080.30130.09350.2661-5.26431.97714.061
32.14580.51820.01534.47910.73040.83920.07480.0202-0.0632-0.1594-0.20150.08410.0433-0.0684-0.00410.20180.0181-0.01450.18460.08170.2084-35.20625.974-1.689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:167 OR RESID 304:307 ) )A1 - 167
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:167 OR RESID 304:307 ) )A304 - 307
3X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )I2 - 110
4X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )H1 - 110
5X-RAY DIFFRACTION3( CHAIN I AND RESID 111:209 ) OR ( CHAIN H AND RESID 111:214 )I111 - 209
6X-RAY DIFFRACTION3( CHAIN I AND RESID 111:209 ) OR ( CHAIN H AND RESID 111:214 )H111 - 214

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