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- PDB-7rni: Discovery of an Anion-Dependent Farnesyltransferase Inhibitor fro... -

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Basic information

Entry
Database: PDB / ID: 7rni
TitleDiscovery of an Anion-Dependent Farnesyltransferase Inhibitor from a Phenotypic Screen
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE/INHIBITOR / PROTEIN INHIBITOR COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / receptor tyrosine kinase binding / response to organic cyclic compound / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Chem-60I / ACETYL GROUP / DIMETHYLALLYL DIPHOSPHATE / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å
AuthorsHruza, A. / Strickland, C.L.
CitationJournal: ACS Med Chem Lett / Year: 2021
Title: Discovery of an Anion-Dependent Farnesyltransferase Inhibitor from a Phenotypic Screen.
Authors: Bukhtiyarova, M. / Cook, E.M. / Hancock, P.J. / Hruza, A.W. / Shaw, A.W. / Adam, G.C. / Barnard, R.J.O. / McKenna, P.M. / Holloway, M.K. / Bell, I.M. / Carroll, S. / Cornella-Taracido, I. / ...Authors: Bukhtiyarova, M. / Cook, E.M. / Hancock, P.J. / Hruza, A.W. / Shaw, A.W. / Adam, G.C. / Barnard, R.J.O. / McKenna, P.M. / Holloway, M.K. / Bell, I.M. / Carroll, S. / Cornella-Taracido, I. / Cox, C.D. / Kutchukian, P.S. / Powell, D.A. / Strickland, C. / Trotter, B.W. / Tudor, M. / Wolkenberg, S. / Li, J. / Tellers, D.M.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6558
Polymers92,8082
Non-polymers8466
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-70 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.058, 169.058, 68.846
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44086.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Production host: Escherichia coli (E. coli)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / Farnesyltransferase / FTase-beta / CAAX farnesyltransferase subunit beta / Ras proteins prenyltransferase subunit beta


Mass: 48722.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Production host: Escherichia coli (E. coli) / References: UniProt: Q02293, protein farnesyltransferase

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Non-polymers , 6 types, 429 molecules

#3: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-60I / [4-[[3-(2,2-dimethylpropyl)-1~{H}-benzimidazol-2-yl]methyl]piperazin-1-yl]-(1,3,5-trimethylpyrazol-4-yl)methanone


Mass: 422.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: PEG 4000, SODIUM ACETATE, KCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.978→43.13 Å / Num. obs: 78499 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 13.4
Reflection shellResolution: 1.978→1.985 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 2 / Num. unique obs: 798 / Rsym value: 1.137 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROC1.1.7data reduction
XDSSeptember 26, 2012data reduction
autoPROC1.1.7data scaling
Aimless0.5.9data scaling
MOLREP11.3.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5M

1o5m


Resolution: 1.978→43.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 3904 -RANDOM
Rwork0.1621 ---
obs0.1633 78475 100 %-
Displacement parametersBiso mean: 43.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.7144 Å20 Å20 Å2
2---1.7144 Å20 Å2
3---3.4287 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.978→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5859 0 53 423 6335
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812042HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8621726HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3559SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2010HARMONIC5
X-RAY DIFFRACTIONt_it6174HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion745SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9908SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 1.98→1.99 Å
RfactorNum. reflection% reflection
Rfree0.1861 55 -
Rwork0.2004 --
obs0.1999 1570 99.15 %
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)
10.79520.02380.04061.4746-0.34110.5465-0.0172-0.1122-0.0512-0.1122-0.02130.1722-0.05120.17220.03840.0323-0.01090.0208-0.0122-0.0037-0.0279195.5423118.864926.1609
21.05630.05520.1630.9442-0.07120.8740.01960.0882-0.06230.0882-0.05490.029-0.06230.0290.03530.0223-0.00650.0161-0.0761-0.0041-0.0778180.8068117.555438.3669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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