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- PDB-9cz5: Crystal structure (II) of human farnesyl pyrophosphate synthase i... -

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Basic information

Entry
Database: PDB / ID: 9cz5
TitleCrystal structure (II) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / enzyme-ligand complex / cryptic pocket binder / isoprenoid biosynthesis
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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
: / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.652 Å
AuthorsPandya, V.R. / Park, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-04281 Canada
CitationJournal: To Be Published
Title: Crystal structure (II) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049
Authors: Pandya, V.R. / Park, J.
History
DepositionAug 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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)44,7656
Polymers43,1451
Non-polymers1,6205
Water1,26170
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,53012
Polymers86,2902
Non-polymers3,24010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9500 Å2
ΔGint-78 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.450, 110.450, 77.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Farnesyl pyrophosphate synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: 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 BL21(DE3) (bacteria)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-A1A05 / {[(6-{4-[(1R)-2,2-difluorocyclopropyl]phenyl}thieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)


Mass: 477.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H15F2N3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.085 M tri-Sodium citrate (pH 5.6), 0.425 M Ammonium sulfate, 0.85 M Lithium sulfate, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.65→63.17 Å / Num. obs: 14144 / % possible obs: 99 % / Redundancy: 9.7 % / Biso Wilson estimate: 64.957 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Rrim(I) all: 0.054 / Net I/σ(I): 28
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 3 / Num. unique obs: 1022 / Rpim(I) all: 0.366 / Rrim(I) all: 1.181 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.652→63.165 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 28.577 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.274
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 708 5.018 %Random
Rwork0.1616 13401 --
all0.164 ---
obs-14109 98.506 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 90.169 Å2
Baniso -1Baniso -2Baniso -3
1--6.555 Å2-0 Å2-0 Å2
2---6.555 Å2-0 Å2
3---13.11 Å2
Refinement stepCycle: LAST / Resolution: 2.652→63.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 101 70 2856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122854
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162600
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.8723901
X-RAY DIFFRACTIONr_angle_other_deg0.6481.7585961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.061512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27810439
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.14610132
X-RAY DIFFRACTIONr_chiral_restr0.0720.2434
X-RAY DIFFRACTIONr_chiral_restr_other3.320.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_nbd_refined0.2370.2712
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22462
X-RAY DIFFRACTIONr_nbtor_refined0.1970.21430
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.298
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1820.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.220
X-RAY DIFFRACTIONr_nbd_other0.1570.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.212
X-RAY DIFFRACTIONr_mcbond_it3.5445.6041353
X-RAY DIFFRACTIONr_mcbond_other3.5445.6041353
X-RAY DIFFRACTIONr_mcangle_it5.38510.0641686
X-RAY DIFFRACTIONr_mcangle_other5.38310.0641687
X-RAY DIFFRACTIONr_scbond_it5.2846.4091501
X-RAY DIFFRACTIONr_scbond_other5.2736.4051494
X-RAY DIFFRACTIONr_scangle_it7.811.7442206
X-RAY DIFFRACTIONr_scangle_other7.7911.7392195
X-RAY DIFFRACTIONr_lrange_it11.3660.033427
X-RAY DIFFRACTIONr_lrange_other11.35960.0363428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.652-2.7210.268420.349730.33610290.8650.80498.63950.292
2.721-2.7950.384510.3159430.31810030.8590.85799.10270.271
2.795-2.8760.316520.2639330.2669920.9330.91499.29430.216
2.876-2.9640.342480.2248990.2299510.9010.94499.57940.186
2.964-3.0610.275460.2198880.2229380.9520.95299.57360.182
3.061-3.1690.311470.1928380.1988860.9380.96899.88710.161
3.169-3.2880.264470.1698160.1748680.9620.97899.4240.15
3.288-3.4220.205400.187860.1828360.960.97898.80380.157
3.422-3.5740.313410.1627530.1688070.9450.98498.38910.147
3.574-3.7470.203480.1476990.1517640.9650.98897.77490.136
3.747-3.9490.195310.1397040.1417470.980.98898.39360.131
3.949-4.1880.123300.1196580.127020.9910.99198.00570.113
4.188-4.4760.187340.1246210.1276630.980.99198.79340.124
4.476-4.8320.206280.1115820.1156230.9660.99197.91330.116
4.832-5.290.157290.1265290.1275720.9860.9997.55250.13
5.29-5.9090.263310.1534840.165250.9670.98498.09520.155
5.909-6.8140.328190.1684390.1754710.9450.98197.23990.17
6.814-8.3210.146210.1583770.1584090.9840.98397.31050.179
8.321-11.6670.141140.1092950.1113270.9890.99394.49540.137
11.667-63.1650.28490.291840.292090.9510.94692.34450.348
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)
18.8272-0.2366-2.77172.7018-0.04473.2012-0.10060.7977-0.3649-0.69320.27170.62340.3678-1.0547-0.17110.2289-0.2011-0.17430.3920.10040.20765.002482.819514.1115
27.0102-0.9418-2.2184.0375-1.29513.60830.03810.0107-0.3399-0.37780.17390.40620.2349-0.3376-0.21190.0472-0.0354-0.03960.04610.03180.064814.529287.116719.2864
36.0225-0.7271-0.11085.5721-2.8444.9962-0.0064-0.7076-0.70220.2318-0.00470.01050.37950.47320.01110.1291-0.01630.02360.37320.10640.147110.572378.758836.5864
45.2928-2.33961.73674.95-2.37283.82540.028-0.6038-0.57790.4345-0.0863-0.06330.60720.22450.05830.3868-0.04220.03180.56140.20310.30568.719771.427742.0904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLF7 - 111
2X-RAY DIFFRACTION2ALLF112 - 179
3X-RAY DIFFRACTION3ALLF182 - 278
4X-RAY DIFFRACTION4ALLF279 - 349

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