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- PDB-1s64: Rat protein geranylgeranyltransferase type-I complexed with L-778... -

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Basic information

Entry
Database: PDB / ID: 1s64
TitleRat protein geranylgeranyltransferase type-I complexed with L-778,123 and a sulfate anion
Components
  • Geranylgeranyl transferase type I beta subunit
  • Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
KeywordsTRANSFERASE / L-778 / 123 / protein geranylgeranyltransferase type-I / protein prenylation / lipid modification / drug
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 / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / heterocyclic compound binding / 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 / receptor tyrosine kinase binding / response to organic cyclic compound / microtubule binding / molecular adaptor activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm
Similarity search - Function
Geranylgeranyl transferase type-1 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 ...Geranylgeranyl transferase type-1 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-778 / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsReid, T.S. / Long, S.B. / Beese, L.S.
CitationJournal: Biochemistry / Year: 2004
Title: Crystallographic Analysis Reveals that Anticancer Clinical Candidate L-778,123 Inhibits Protein Farnesyltransferase and Geranylgeranyltransferase-I by Different Binding Modes.
Authors: Reid, T.S. / Long, S.B. / Beese, L.S.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_conn.ptnr2_label_seq_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 I alpha subunit
B: Geranylgeranyl transferase type I beta subunit
C: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
D: Geranylgeranyl transferase type I beta subunit
E: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
F: Geranylgeranyl transferase type I beta subunit
G: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
H: Geranylgeranyl transferase type I beta subunit
I: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
J: Geranylgeranyl transferase type I beta subunit
K: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
L: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)524,28145
Polymers519,38612
Non-polymers4,89533
Water24,7711375
1
A: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
B: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3276
Polymers86,5642
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-81 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
D: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3988
Polymers86,5642
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-101 kcal/mol
Surface area25510 Å2
MethodPISA
3
E: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
F: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3627
Polymers86,5642
Non-polymers7985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-93 kcal/mol
Surface area25840 Å2
MethodPISA
4
G: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
H: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3988
Polymers86,5642
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-103 kcal/mol
Surface area25720 Å2
MethodPISA
5
I: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
J: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3988
Polymers86,5642
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-104 kcal/mol
Surface area25930 Å2
MethodPISA
6
K: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
L: Geranylgeranyl transferase type I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3988
Polymers86,5642
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-103 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.153, 268.681, 184.622
Angle α, β, γ (deg.)90.00, 131.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11J-415-

HOH

21L-545-

HOH

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit / CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type ...CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type I protein geranyl-geranyltransferase alpha subunit / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 6 / Fragment: alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein
Geranylgeranyl transferase type I beta subunit / Type I protein geranyl-geranyltransferase beta subunit / GGTase-I-beta


Mass: 42466.176 Da / Num. of mol.: 6 / Fragment: beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PGGT1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53610, protein geranylgeranyltransferase type I

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Non-polymers , 6 types, 1408 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-778 / 4-[(5-{[4-(3-CHLOROPHENYL)-3-OXOPIPERAZIN-1-YL]METHYL}-1H-IMIDAZOL-1-YL)METHYL]BENZONITRILE / L-778,123


Mass: 405.880 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H20ClN5O
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1375 / 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: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 290 K / pH: 6.3
Details: 1.3 M ammonium sulfate, 175 mM NaCitrate pH 6.5, 100 mM MES pH 6.3, 20 mM DTT, 1uM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 6.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2001 / Details: BENT CONICAL SI-MIRROR (RH COATING)
RadiationMonochromator: BENT GE(III) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 320017 / Num. obs: 300151 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.256 / % possible all: 85.6

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N4Q

1n4q


Resolution: 2.55→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4876426.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.213 15041 5 %RANDOM
Rwork0.192 ---
obs0.192 298789 93.4 %-
all-320017 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3673 Å2 / ksol: 0.359785 e/Å3
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1--6.78 Å20 Å2-3.59 Å2
2--10.53 Å20 Å2
3----3.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32069 0 291 1375 33735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it9.342.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 2311 5 %
Rwork0.304 43615 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAM778.TOP
X-RAY DIFFRACTION4778.PARION.TOP
X-RAY DIFFRACTION5MES.PARMES.TOP

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