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- PDB-4l2x: Crystal structure of human FPPS in complex with magnesium, CL0213... -

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Basic information

Entry
Database: PDB / ID: 4l2x
TitleCrystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome / mitochondrial matrix / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Chem-YL2 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsPark, J. / Leung, C.-Y. / Tsantrizos, Y.S. / Berghuis, A.M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition.
Authors: Leung, C.Y. / Park, J. / De Schutter, J.W. / Sebag, M. / Berghuis, A.M. / Tsantrizos, Y.S.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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
F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8356
Polymers43,1451
Non-polymers6905
Water27015
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,67012
Polymers86,2902
Non-polymers1,38010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5250 Å2
ΔGint-83 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.340, 111.340, 68.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-YL2 / ({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)


Mass: 441.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O6P2S
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG8000, 20% glycerol, 0.16 M magnesium acetate, 0.08 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 5, 2013
RadiationMonochromator: ACCEL/Bruker DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 14627 / Num. obs: 14376 / % possible obs: 98.3 % / Redundancy: 9.48 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 9.52 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 6.07 / Num. unique all: 1069 / % possible all: 93.8

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0032phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4H5D

4h5d


Resolution: 2.55→35.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.554 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 704 5 %RANDOM
Rwork0.20083 ---
all0.20355 13394 --
obs0.20355 13394 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.961 Å2
Baniso -1Baniso -2Baniso -3
1--6.17 Å20 Å20 Å2
2---6.17 Å20 Å2
3---12.35 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 40 15 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022784
X-RAY DIFFRACTIONr_bond_other_d0.0030.022562
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9813795
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0015858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46124.64125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0661512
X-RAY DIFFRACTIONr_chiral_restr0.080.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
LS refinement shellResolution: 2.55→2.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 53 -
Rwork0.34 842 -
obs-895 85.32 %

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