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- PDB-2r2l: Structure of Farnesyl Protein Transferase bound to PB-93 -

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Basic information

Entry
Database: PDB / ID: 2r2l
TitleStructure of Farnesyl Protein Transferase bound to PB-93
Components(Farnesyltransferase subunit ...) x 2
KeywordsTRANSFERASE / Malaria / FPT / Metal-binding / Phosphorylation / Prenyltransferase / Zinc
Function / homology
Function and homology information


skeletal muscle acetylcholine-gated channel clustering / 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 ...skeletal muscle acetylcholine-gated channel clustering / 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 / response to organic cyclic compound / receptor tyrosine kinase binding / 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 / plasma membrane / 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
FARNESYL DIPHOSPHATE / Chem-PB9 / Protein farnesyltransferase subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.23 Å
AuthorsStrickland, C.O. / Voorhis, W.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2007
Title: Efficacy, pharmacokinetics, and metabolism of tetrahydroquinoline inhibitors of Plasmodium falciparum protein farnesyltransferase.
Authors: Van Voorhis, W.C. / Rivas, K.L. / Bendale, P. / Nallan, L. / Horney, C. / Barrett, L.K. / Bauer, K.D. / Smart, B.P. / Ankala, S. / Hucke, O. / Verlinde, C.L. / Chakrabarti, D. / Strickland, ...Authors: Van Voorhis, W.C. / Rivas, K.L. / Bendale, P. / Nallan, L. / Horney, C. / Barrett, L.K. / Bauer, K.D. / Smart, B.P. / Ankala, S. / Hucke, O. / Verlinde, C.L. / Chakrabarti, D. / Strickland, C. / Yokoyama, K. / Buckner, F.S. / Hamilton, A.D. / Williams, D.K. / Lombardo, L.J. / Floyd, D. / Gelb, M.H.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Farnesyltransferase subunit alpha
B: Farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8075
Polymers82,7962
Non-polymers1,0113
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.614, 171.614, 69.155
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Farnesyltransferase subunit ... , 2 types, 2 molecules AB

#1: Protein Farnesyltransferase subunit alpha /


Mass: 37916.566 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: Q5RKJ4, UniProt: Q04631*PLUS
#2: Protein Farnesyltransferase subunit beta / / CAAX farnesyltransferase subunit beta / RAS proteins prenyltransferase beta / FTase-beta


Mass: 44879.297 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 , 4 types, 537 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#5: Chemical ChemComp-PB9 / methyl 4-{[{(3S)-6-cyano-1-[(1-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroquinolin-3-yl}(pyridin-2-ylsulfonyl)amino]methyl}piperidine-1-carboxylate


Mass: 563.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33N7O4S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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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: 3.55 Å3/Da / Density % sol: 65.36 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: Max Flux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→20 Å / Num. all: 56752 / Num. obs: 56633 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1 / Net I/σ(I): 17.3
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2780 / Rsym value: 0.308 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
JDirectordata collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 2.23→20 Å / FOM work R set: 0.856
RfactorNum. reflection% reflection
Rfree0.221 2872 5.1 %
Rwork0.189 --
obs-56589 99.6 %
Displacement parametersBiso mean: 42.366 Å2
Refinement stepCycle: LAST / Resolution: 2.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5833 0 65 534 6432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.26
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parasch0093.protopsch0093.pro
X-RAY DIFFRACTION2parafpp.protopfpp.pro
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.paramMSI_CNX_TOPPAR:water.top
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.paramMSI_CNX_TOPPAR:ion.top
X-RAY DIFFRACTION5MSI_CNX_TOPPAR:protein_rep.paramMSI_CNX_TOPPAR:protein.top

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