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- PDB-9glz: KRas-G12D-GMPPnP in complex with the nanobody KM12-AM -

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Basic information

Entry
Database: PDB / ID: 9glz
TitleKRas-G12D-GMPPnP in complex with the nanobody KM12-AM
Components
  • GTPase KRas
  • nanobody KM12-AM
KeywordsHYDROLASE / GTPase / SIGNALING PROTEIN / SMALL G-PROTEIN
Function / homology
Function and homology information


small monomeric GTPase / GTPase activity / GTP binding / signal transduction / plasma membrane
Similarity search - Function
Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / small monomeric GTPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOstermann, N. / Zink, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Identification and characterization of binders to a cryptic and functional pocket in KRAS.
Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, ...Authors: Beyer, K.S. / Klein, J. / Katz, S. / Welker, P. / Lanter, M. / Guthy, D. / Pollehn, K. / Gluck-Gade, A. / Bleu, M. / Desogus, J. / Hattenberger, M. / Borrello, D. / Abdul Rahman, W. / Zink, F. / Ostermann, N. / Jahnke, W. / Dumelin, C.E. / Leder, L. / Esser, O. / Muller, L. / Marzinzik, A. / Cebe, R. / Muller, K. / Galli, G.G. / Tordella, L. / Cotesta, S. / Brachmann, S.M. / Maira, S.M.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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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: nanobody KM12-AM
D: nanobody KM12-AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3738
Polymers68,2804
Non-polymers1,0934
Water3,171176
1
A: GTPase KRas
C: nanobody KM12-AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6864
Polymers34,1402
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-23 kcal/mol
Surface area13100 Å2
2
B: GTPase KRas
D: nanobody KM12-AM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6864
Polymers34,1402
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-23 kcal/mol
Surface area12940 Å2
Unit cell
Length a, b, c (Å)84.072, 122.32, 105.615
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTPase KRas / Ki-Ras


Mass: 19364.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Kras, DROARD_R09727 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K5XXT4, small monomeric GTPase
#2: Antibody nanobody KM12-AM


Mass: 14775.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1000, 0.2 M LiNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000043 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000043 Å / Relative weight: 1
ReflectionResolution: 1.76→61.16 Å / Num. obs: 43995 / % possible obs: 94.1 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.3
Reflection shellResolution: 1.76→1.88 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2200 / % possible all: 56.4

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Processing

Software
NameVersionClassificationNB
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKNG

Resolution: 2.1→24.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.281 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1638 -RANDOM
Rwork0.2391 ---
obs0.241 31891 99.3 %-
Displacement parametersBiso mean: 43.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.8764 Å20 Å20 Å2
2--2.7482 Å20 Å2
3----1.8718 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 66 176 4431
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084332HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.935884HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1469SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes746HARMONIC5
X-RAY DIFFRACTIONt_it4332HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion583SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3337SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion17.73
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection% reflection
Rfree0.3314 36 -
Rwork0.3058 --
obs0.3072 638 89.87 %
Refinement TLS params.

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)
12.6090.2056-0.80010.86430.01711.7790.19130.0638-0.06960.0638-0.09370.2688-0.06960.2688-0.0976-0.0488-0.01310.02040.052-0.009-0.0598-14.4649-19.6396-14.3275
21.5750.397-0.42692.0519-0.56082.49110.05440.0693-0.19690.06930.0863-0.0899-0.1969-0.0899-0.1407-0.01440.00240.0287-0.03030.0201-0.0297-21.7368-17.388515.7713
31.8556-1.0246-0.32046.6995.17068.96670.0112-0.51960.0576-0.5196-1.404-1.33840.0576-1.33841.3928-0.48390.055-0.08860.0385-0.42360.1446-51.945-11.6355-6.3554
43.4326-3.3064-2.823311.28016.6949.08950.1440.65330.43950.6533-0.5133-0.47130.4395-0.47130.3692-0.1017-0.08530.0333-0.0357-0.0024-0.0902-41.008-13.5216-3.374
57.53830.0194-4.093814.7732.641419.00240.20061.63271.21021.6327-1.4321-1.34091.2102-1.34091.2315-0.2825-0.36660.3697-0.1403-0.29290.0497-49.0149-17.35650.3596
65.3915-1.8823-3.46998.42337.19066.65240.1729-0.6506-0.3146-0.6506-0.3705-0.054-0.3146-0.0540.1975-0.05160.037-0.0226-0.0241-0.003-0.1218-37.7398-10.997-9.283
710.3190.1273-2.462414.00392.13334.59250.264-0.2147-0.1755-0.2147-1.1579-1.0757-0.1755-1.07570.8938-0.26910.0691-0.04480.0549-0.41270.0175-49.1242-4.522-2.2675
89.47774.0465-8.45870.7017-2.317519.7959-0.09230.17880.71790.1788-0.27540.57970.71790.57970.3678-0.4939-0.0351-0.0639-0.06510.2295-0.125618.8297-10.27534.0333
94.43087.4068-5.181516.5342-8.73128.98930.52020.0008-0.10990.0008-1.11261.007-0.10991.0070.5924-0.21130.0019-0.01350.31650.1111-0.27695.4956-12.66876.0578
1011.2286-0.7913-5.69247.61694.746200.7367-0.80160.7342-0.8016-0.896-0.1350.7342-0.1350.1592-0.1860.29920.0519-0.0640.208-0.189714.6602-16.12273.0675
111.9999-1.010.75677.7673-8.73129.63930.54691.0974-0.73091.0974-1.08590.9027-0.73090.90270.539-0.0633-0.33370.06440.2425-0.0643-0.24591.8586-9.095210.3206
126.54871.6324-2.897.60262.288200.2410.29880.42680.2988-0.64740.63370.42680.63370.4065-0.1958-0.34620.06090.73210.4559-0.032714.0299-4.13912.5027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|*}A1 - 168
2X-RAY DIFFRACTION1{A|*}A1001
3X-RAY DIFFRACTION2{B|*}B1 - 168
4X-RAY DIFFRACTION2{B|*}B1001
5X-RAY DIFFRACTION3{C|2 - 31}C2 - 31
6X-RAY DIFFRACTION4{C|32 - 61}C32 - 61
7X-RAY DIFFRACTION5{C|62 - 90}C62 - 90
8X-RAY DIFFRACTION6{C|91 - 113}C91 - 113
9X-RAY DIFFRACTION7{C|114 - 121}C114 - 121
10X-RAY DIFFRACTION8{D|3 - 24}D3 - 24
11X-RAY DIFFRACTION9{D|32 - 61}D32 - 61
12X-RAY DIFFRACTION10{D|65 - 90}D65 - 90
13X-RAY DIFFRACTION11{D|91 - 113}D91 - 113
14X-RAY DIFFRACTION12{D|114 - 122}D114 - 122

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