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- PDB-1nl4: Crystal Structure of Rat Farnesyl Transferase in Complex With A P... -

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Basic information

Entry
Database: PDB / ID: 1nl4
TitleCrystal Structure of Rat Farnesyl Transferase in Complex With A Potent Biphenyl Inhibitor
Components
  • Protein farnesyltransferase alpha subunit
  • Protein farnesyltransferase beta subunit
KeywordsTRANSFERASE / Prenyltransferase
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / regulation of fibroblast proliferation / regulation of microtubule-based movement / geranylgeranyl diphosphate synthase activity / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / wound healing / receptor tyrosine kinase binding / lipid metabolic process / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / molecular adaptor activity / cell population proliferation / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / 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 alpha-alpha toroid domain / 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 alpha-alpha toroid domain / 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-FTL / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID / 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: 2.7 Å
AuthorsCurtin, M.L. / Florjancic, A.S. / Cohen, J. / Gu, W.-J. / Frost, D.J. / Muchmore, S.W. / Sham, H.L.
CitationJournal: BIOORG.MED.CHEM.LETT. / Year: 2003
Title: Novel and Selective Imidazole-containing Biphenyl Inhibitors of Protein Farnesyltransferase
Authors: Curtin, M.L. / Florjancic, A.S. / Cohen, J. / Gu, W.-J. / Frost, D.J. / Muchmore, S.W. / Sham, H.L.
History
DepositionJan 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 999sequence Author indicates that this represents an inconsequential mutation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein farnesyltransferase alpha subunit
B: Protein farnesyltransferase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3415
Polymers82,5142
Non-polymers8273
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-60 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.620, 168.620, 69.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein farnesyltransferase alpha subunit / CAAX farnesyltransferase alpha subunit / RAS proteins prenyltransferase alpha / FTase-alpha


Mass: 37634.293 Da / Num. of mol.: 1 / Fragment: residue 55-366 / Mutation: I156T
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, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein Protein farnesyltransferase beta subunit / CAAX farnesyltransferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 44879.297 Da / Num. of mol.: 1 / Fragment: residue 23-423
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, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HFP / ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID


Mass: 308.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33O4P
#5: Chemical ChemComp-FTL / 4-[(3-CYANO-BENZYL)-(3-METHYL-3H-IMIDAZOL-4-YLMETHYL)-AMINO]-2-NAPHTHALEN-1-YL-BENZONITRILE


Mass: 453.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H23N5

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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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: equilibriate equal volumes of 10mg/ml protein stock solution (with 50mM Tris, 1mM DTT, 1mM NaN3, 5 mM ZnCl2-pH 8.2) and well solution containing 100mM KCl, 100mM Sodium Acetate, at pH 4.8, ...Details: equilibriate equal volumes of 10mg/ml protein stock solution (with 50mM Tris, 1mM DTT, 1mM NaN3, 5 mM ZnCl2-pH 8.2) and well solution containing 100mM KCl, 100mM Sodium Acetate, at pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Strickland, C.L., (19999) J. Med. Chem., 42, 2125.

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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 / Date: Oct 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 26759 / Num. obs: 26759 / % possible obs: 85 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.056 / Rsym value: 0.056
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % possible obs: 98 % / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2140 -RANDOM
Rwork0.229 ---
all0.231 26759 --
obs0.231 26759 85 %-
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 56 0 5871
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS

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