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- PDB-4gtp: FTase in complex with BMS analogue 16 -

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Basic information

Entry
Database: PDB / ID: 4gtp
TitleFTase in complex with BMS analogue 16
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 / 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-7TP / 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: 2.75 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)93,2209
Polymers91,8472
Non-polymers1,3737
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-13 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.650, 171.650, 70.005
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, 135 molecules

#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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-7TP / 5-{(3R)-3-(4-hydroxybenzyl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-7-yl}furan-2-carbaldehyde


Mass: 612.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H32N4O6S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
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 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→29.91 Å / Num. all: 30875 / Num. obs: 30855 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 17.8
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.36 / % possible all: 100

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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: 2.75→29.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.052 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22565 1557 5 %RANDOM
Rwork0.17671 ---
obs0.17922 29277 99.97 %-
all-30875 --
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 max: 140.5 Å2 / Biso mean: 42.888 Å2 / Biso min: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 85 128 6066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226097
X-RAY DIFFRACTIONr_bond_other_d00.024132
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9628281
X-RAY DIFFRACTIONr_angle_other_deg4.0383.0019969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68923.987311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.313151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361542
X-RAY DIFFRACTIONr_chiral_restr0.1080.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026770
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021253
X-RAY DIFFRACTIONr_nbd_refined0.2640.21928
X-RAY DIFFRACTIONr_nbd_other0.2550.24558
X-RAY DIFFRACTIONr_nbtor_refined0.2080.23029
X-RAY DIFFRACTIONr_nbtor_other0.1110.23004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2265
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it0.8171.53590
X-RAY DIFFRACTIONr_mcbond_other01.51441
X-RAY DIFFRACTIONr_mcangle_it1.52425795
X-RAY DIFFRACTIONr_scbond_it2.13132507
X-RAY DIFFRACTIONr_scangle_it3.344.52485
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 107 -
Rwork0.272 2154 -
obs--100 %
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)
10.4677-0.614-0.12641.0940.36070.4793-0.0251-0.0343-0.03930.0075-0.01210.11390.1211-0.00350.03720.01070.06720.0461-0.06830.0263-0.021754.087438.02442.6588
20.39890.0034-0.13140.72960.11090.8820.02330.05030.0541-0.0895-0.0635-0.06790.03040.1180.0402-0.06970.07440.03650.01110.0661-0.025462.264650.5315-9.3533
322.5221-6.90210.82582.6814-2.14267.64190.2949-2.1251-0.9858-1.835-0.50040.6657-0.5466-0.18020.2055-0.00310.002-0.0019-0.00080.0010.001951.849150.2218-0.3562
40000000000000000.0012-0.0011-0.00280.0007-0.00120.00252.544847.4125-9.7882
534.11755.5681-10.00383.8253-3.6684.35370.4133-0.55270.557-0.1785-0.67310.53150.12290.14830.2598-0.0020.0043-0.0019-0.0003-0.0009-0.002756.007945.2708-2.324
61.1163-0.2902-6.98480.07551.81643.70560.04250.5580.60990.9362-0.20230.3329-0.8088-0.05070.15980.00050.00060.0035-0.00040.0009-0.001951.483751.6619-4.1882
70.2356-0.1345-0.10580.58850.27250.4949-0.02150.0093-0.0184-0.03560.03020.06940.01770.023-0.0086-0.04610.07980.03350.00210.0601-0.015655.57646.2512-5.4874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 369
2X-RAY DIFFRACTION2B21 - 423
3X-RAY DIFFRACTION3A401
4X-RAY DIFFRACTION3B504 - 506
5X-RAY DIFFRACTION4B501
6X-RAY DIFFRACTION5B502
7X-RAY DIFFRACTION6B503
8X-RAY DIFFRACTION7A501 - 557
9X-RAY DIFFRACTION7B601 - 671

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