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- PDB-1mzc: Co-Crystal Structure Of Human Farnesyltransferase With Farnesyldi... -

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Basic information

Entry
Database: PDB / ID: 1mzc
TitleCo-Crystal Structure Of Human Farnesyltransferase With Farnesyldiphosphate and Inhibitor Compound 33a
Components(Protein Farnesyltransferase ...) x 2
KeywordsTRANSFERASE / ALPHA-ALPHA BARREL / INHIBITOR / FTASE / PFTASE / FPP / CAAX / RAS
Function / homology
Function and homology information


skeletal muscle acetylcholine-gated channel clustering / 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 ...skeletal muscle acetylcholine-gated channel clustering / 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 microtubule-based movement / positive regulation of skeletal muscle acetylcholine-gated channel clustering / acetyltransferase activator activity / microtubule associated complex / Apoptotic cleavage of cellular proteins / positive regulation of Rac protein signal transduction / alpha-tubulin binding / positive regulation of cell cycle / peptide binding / transforming growth factor beta receptor signaling pathway / receptor tyrosine kinase binding / lipid metabolic process / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / microtubule binding / molecular adaptor activity / Potential therapeutics for SARS / positive regulation of cell population proliferation / enzyme binding / zinc ion binding / plasma membrane / cytoplasm / cytosol
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
sucrose / Chem-BNE / FARNESYL DIPHOSPHATE / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsdeSolms, S.J. / Ciccarone, T.M. / MacTough, S.C. / Shaw, A.W. / Buser, C.A. / Ellis-Hutchings, M. / Fernandes, C. / Hamilton, K.A. / Huber, H.E. / Kohl, N.E. ...deSolms, S.J. / Ciccarone, T.M. / MacTough, S.C. / Shaw, A.W. / Buser, C.A. / Ellis-Hutchings, M. / Fernandes, C. / Hamilton, K.A. / Huber, H.E. / Kohl, N.E. / Lobell, R.B. / Robinson, R.G. / Tsou, N.N. / Walsh, E.S. / Graham, S.L. / Beese, L.S. / Taylor, J.S.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Dual Protein Farnesyltransferase-Geranylgeranyltransferase-I Inhibitors as Potential Cancer Chemotherapeutic Agents.
Authors: DeSolms, S.J. / Ciccarone, T.M. / MacTough, S.C. / Shaw, A.W. / Buser, C.A. / Ellis-Hutchings, M. / Fernandes, C. / Hamilton, K.A. / Huber, H.E. / Kohl, N.E. / Lobell, R.B. / Robinson, R.G. ...Authors: DeSolms, S.J. / Ciccarone, T.M. / MacTough, S.C. / Shaw, A.W. / Buser, C.A. / Ellis-Hutchings, M. / Fernandes, C. / Hamilton, K.A. / Huber, H.E. / Kohl, N.E. / Lobell, R.B. / Robinson, R.G. / Tsou, N.N. / Walsh, E.S. / Graham, S.L. / Beese, L.S. / Taylor, J.S.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)94,9496
Polymers93,6872
Non-polymers1,2624
Water12,665703
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-59 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.385, 178.385, 64.579
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe asymmetric unit contains one complete biological unit (heterodimer)

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Components

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Protein Farnesyltransferase ... , 2 types, 2 molecules AB

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


Mass: 44864.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49354, 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: 48822.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49356, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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Sugars , 1 types, 1 molecules

#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 706 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#6: Chemical ChemComp-BNE / 2-[3-(3-ETHYL-1-METHYL-2-OXO-AZEPAN-3-YL)-PHENOXY]-4-[1-AMINO-1-(1-METHYL-1H-IMIDIZOL-5-YL)-ETHYL]-BENZONITRILE


Mass: 471.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33N5O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG8K NH4OAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMDMSO1drop
3200-400 mMammonium acetate1reservoir
412-14 %PEG80001reservoirpH5.3-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 17, 2000 / Details: Mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→36.7 Å / Num. all: 75205 / Num. obs: 75205 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 3242 / Rsym value: 0.341 / % possible all: 82.1
Reflection
*PLUS
Lowest resolution: 37 Å / % possible obs: 94.7 % / Num. measured all: 278618 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 82.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCQ

1jcq


Resolution: 2→36.7 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3785 5 %RANDOM
Rwork0.177 ---
all0.177 75230 --
obs0.177 75205 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.8835 Å2 / ksol: 0.399425 e/Å3
Displacement parametersBiso mean: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å22.37 Å20 Å2
2--1.2 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 83 703 6663
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.71.5
X-RAY DIFFRACTIONc_mcangle_it1.172
X-RAY DIFFRACTIONc_scbond_it1.182
X-RAY DIFFRACTIONc_scangle_it1.852.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 569 5.1 %
Rwork0.232 10613 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SUCROSE.PARSUCROSE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5FPP.PARFPP.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 37 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it0.7

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