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- PDB-4gtr: FTase in complex with BMS analogue 13 -

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Basic information

Entry
Database: PDB / ID: 4gtr
TitleFTase in complex with BMS analogue 13
Components
  • Protein farnesyltransferase subunit betaFarnesyltransferase
  • 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 / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...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 / 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 / receptor tyrosine kinase binding / response to organic cyclic compound / 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-7TR / 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: 2.2 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)93,1728
Polymers91,8472
Non-polymers1,3256
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-10 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.275, 172.275, 69.607
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 / Farnesyltransferase / 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, 411 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / 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-7TR / 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 diethylcarbamate


Mass: 642.768 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N6O5S
#6: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
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: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→29.91 Å / Num. all: 60055 / Num. obs: 60023 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 40.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 18.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.387 / % possible all: 99.9

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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: PDB ENTRY 3EU5

3eu5


Resolution: 2.2→29.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.825 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21229 2988 5 %RANDOM
Rwork0.17871 ---
obs0.18039 57015 99.96 %-
all-60055 --
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: 42.553 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 83 405 6322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226092
X-RAY DIFFRACTIONr_bond_other_d00.024095
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9618279
X-RAY DIFFRACTIONr_angle_other_deg4.12639921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17123.961308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.061151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2881541
X-RAY DIFFRACTIONr_chiral_restr0.0850.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026769
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021253
X-RAY DIFFRACTIONr_nbd_refined0.2390.21800
X-RAY DIFFRACTIONr_nbd_other0.2420.24247
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22971
X-RAY DIFFRACTIONr_nbtor_other0.110.22657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7291.53594
X-RAY DIFFRACTIONr_mcbond_other01.51443
X-RAY DIFFRACTIONr_mcangle_it1.35225800
X-RAY DIFFRACTIONr_scbond_it1.99632498
X-RAY DIFFRACTIONr_scangle_it3.0874.52476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 211 -
Rwork0.233 4206 -
obs--99.91 %
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)
10.162-0.28730.23220.6296-0.18950.7451-0.03260.0470.04170.0025-0.01190.01740.10660.16740.04450.0130.0740.0389-0.0610.0305-0.0225-59.9711-27.4041-2.1568
20.4126-0.08340.05130.1191-0.16681.4993-0.0628-0.03180.02520.047-0.01130.03490.2762-0.10890.0740.0582-0.01460.0549-0.1219-0.0023-0.0256-74.8565-28.720410.2072
32.0640.1133-0.73020.5127-0.94631.8797-0.24850.20470.118-0.06310.05510.0547-0.15080.04960.19340.00040.0010.0021-0.00080.0010.0004-71.1697-19.5714.7734
4000000000000000-0.00640.02210.021-0.00630.005-0.0057-67.3879-21.832110.4397
530.577512.379110.56219.65884.51023.66020.04160.0925-0.0310.1692-0.20020.5074-0.08290.25710.15860.00090.00030.00070.0001-0.00030-66.9347-26.01463.0781
65.118515.60311347.614839.784933.4981-0.4774-0.4848-0.61560.22330.0492-1.4154-1.62480.88890.4282-0.00150.00030.0014-0.0005-0.00020-68.4001-18.90354.6655
70.1649-0.08620.05090.2164-0.06050.6945-0.0367-0.0080.01340.029-0.00480.01710.10890.05270.04140.0170.0290.0408-0.09250.0125-0.0066-66.901-23.983.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 369
2X-RAY DIFFRACTION2B21 - 423
3X-RAY DIFFRACTION3B502
4X-RAY DIFFRACTION4B501
5X-RAY DIFFRACTION5B503
6X-RAY DIFFRACTION6A401
7X-RAY DIFFRACTION6B504 - 505
8X-RAY DIFFRACTION7A501 - 699
9X-RAY DIFFRACTION7B601 - 806

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