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- PDB-1x81: Farnesyl transferase structure of Jansen compound -

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Basic information

Entry
Database: PDB / ID: 1x81
TitleFarnesyl transferase structure of Jansen compound
Components
  • Protein farnesyltransferase beta subunit
  • Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
KeywordsTRANSFERASE / fanesyltransferase
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 farnesylation / protein geranylgeranyltransferase type I / 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 farnesylation / protein geranylgeranyltransferase type I / 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 / Protein prenylyltransferase / 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 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / 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 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-JAN / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsLi, Q. / Claiborne, A. / Li, T. / Hasvold, L. / Stoll, V.S. / Muchmore, S. / Jakob, C.G. / Gu, W. / Cohen, J. / Hutchins, C. ...Li, Q. / Claiborne, A. / Li, T. / Hasvold, L. / Stoll, V.S. / Muchmore, S. / Jakob, C.G. / Gu, W. / Cohen, J. / Hutchins, C. / Frost, D. / Rosenberg, S.H. / Sham, H.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: Design, synthesis, and activity of 4-quinolone and pyridone compounds as nonthiol-containing farnesyltransferase inhibitors.
Authors: Li, Q. / Claiborne, A. / Li, T. / Hasvold, L. / Stoll, V.S. / Muchmore, S. / Jakob, C.G. / Gu, W. / Cohen, J. / Hutchins, C. / Frost, D. / Rosenberg, S.H. / Sham, H.L.
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,0624
Polymers82,5082
Non-polymers5552
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-63 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.086, 170.086, 69.133
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 38028.766 Da / Num. of mol.: 1 / Fragment: residues 55-369 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase beta subunit / CAAX farnesyltransferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 44478.828 Da / Num. of mol.: 1 / Fragment: residues 22-418 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q02293, protein farnesyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-JAN / 6-[(S)-AMINO(4-CHLOROPHENYL)(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-4-(3-CHLOROPHENYL)-1-METHYLQUINOLIN-2(1H)-ONE / R115777 / TIPIFARNIB / Tipifarnib


Mass: 489.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22Cl2N4O / Comment: inhibitor*YM

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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: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5 / Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 13627 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.72 Å / % possible all: 92

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98refinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.292 1068 7.8
Rwork0.223 --
obs-13627 -
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 35 0 5849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d1.7
X-RAY DIFFRACTIONx_dihedral_angle_d19.4
X-RAY DIFFRACTIONx_improper_angle_d0.86
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.33 178 -
Rwork0.26 --
obs-2042 92 %

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