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- PDB-4gto: FTase in complex with BMS analogue 14 -

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Basic information

Entry
Database: PDB / ID: 4gto
TitleFTase in complex with BMS analogue 14
Components
  • Protein farnesyltransferase subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein prenylation / inhibitor / 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 farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase ...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 / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / regulation of fibroblast proliferation / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / : / farnesyltranstransferase 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 / 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 / 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-7TO / FARNESYL 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: 2.15 Å
AuthorsGuo, Z. / Stigter, E.A. / Bon, R.S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Development of Selective, Potent RabGGTase Inhibitors
Authors: Stigter, E.A. / Guo, Z. / Bon, R.S. / Wu, Y.W. / Choidas, A. / Wolf, A. / Menninger, S. / Waldmann, H. / Blankenfeldt, W. / Goody, R.S.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0496
Polymers91,8472
Non-polymers1,2024
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-19 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.704, 172.704, 69.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 44098.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: pGATEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase subunit beta / FTase-beta / CAAX farnesyltransferase subunit beta / Ras proteins prenyltransferase subunit beta


Mass: 47749.340 Da / Num. of mol.: 1 / Fragment: C-terminal 10 residues deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON-PLUS RIL (DE3) / References: UniProt: Q02293, protein farnesyltransferase

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Non-polymers , 5 types, 566 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-7TO / 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl trifluoromethanesulfonate


Mass: 675.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28F3N5O6S2
#5: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→29.91 Å / Num. all: 64604 / Num. obs: 63953 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.054 / Net I/σ(I): 15.9
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.365 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASESphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU5

3eu5


Resolution: 2.15→29.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.307 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.629 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22518 3190 5 %RANDOM
Rwork0.18763 ---
obs0.18955 60748 99.02 %-
all-64604 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 65 562 6475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226109
X-RAY DIFFRACTIONr_bond_other_d00.024111
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.968318
X-RAY DIFFRACTIONr_angle_other_deg4.1463.0019953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47424.097310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.026151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8771540
X-RAY DIFFRACTIONr_chiral_restr0.0740.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026816
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021253
X-RAY DIFFRACTIONr_nbd_refined0.2870.22100
X-RAY DIFFRACTIONr_nbd_other0.2730.24492
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22969
X-RAY DIFFRACTIONr_nbtor_other0.1080.22617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6891.53625
X-RAY DIFFRACTIONr_mcbond_other3.1861.51457
X-RAY DIFFRACTIONr_mcangle_it2.80625844
X-RAY DIFFRACTIONr_scbond_it2.71232484
X-RAY DIFFRACTIONr_scangle_it4.354.52468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 242 -
Rwork0.258 4454 -
obs--99.87 %
Refinement TLS params.

Method: refined / 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)
10.4681-0.022-0.16810.0140.07290.3854-0.0321-0.0105-0.00950.03440.0090.08410.01150.13280.0231-0.066-0.0134-0.00360.06580.0475-0.0037-6.125266.08849.705
20.1436-0.0624-0.13940.0465-0.03840.6405-0.00880.0321-0.032-0.0038-0.03180.0512-0.13480.11410.0406-0.0152-0.0648-0.02140.02440.0315-0.0137-12.540979.5312-2.6055
30.04960.0272-0.0260.0299-0.02310.01890.00010.00010.00070.0005-0.0007-0.00020.0009-0.00050.0006000000-26.027168.9404-0.5045
40000000000000000.009-0.00090.00060.00930.00070.0109-14.470469.5729-2.375
5116.0436.2606-63.346930.64687.4027101.1939-0.07011.9787-1.0309-0.58120.27280.72951.1359-0.5879-0.20270.0028-0.0053-0.00010.0064-0.00290.0035-10.089967.20334.0198
610.41243.4723-13.29591.1697-4.209921.2637-0.2734-0.52970.29341.165-0.22010.7830.63080.79110.4935-0.0013-0.00210.00130-0.0009-0.0002-17.208472.03023.7531
70.4535-0.0004-0.17690.1754-0.02530.5346-0.00180.01570.0169-0.0033-0.0134-0.0047-0.03550.0970.01520.0071-0.022-0.01010.04940.0180.0525-11.577872.52993.9487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 370
2X-RAY DIFFRACTION2B18 - 423
3X-RAY DIFFRACTION3B504
4X-RAY DIFFRACTION4B501
5X-RAY DIFFRACTION5B503
6X-RAY DIFFRACTION6B502
7X-RAY DIFFRACTION7A401 - 668
8X-RAY DIFFRACTION7B601 - 894

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