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- PDB-9cyz: Crystal structure of human farnesyl pyrophosphate synthase in com... -

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Basic information

Entry
Database: PDB / ID: 9cyz
TitleCrystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL02134
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
Chem-YL2 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.302 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: J.Struct.Biol. / Year: 2026
Title: Discovery and computational characterization of a novel cryptic pocket in human farnesyl pyrophosphate synthase.
Authors: Pandya, V. / Wilson, K.A. / Leung, C.Y. / Tsantrizos, Y.S. / Park, J.
History
DepositionAug 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)44,7537
Polymers43,1451
Non-polymers1,6086
Water1,910106
1
F: Farnesyl pyrophosphate synthase
hetero molecules

F: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,50614
Polymers86,2902
Non-polymers3,21612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5710 Å2
ΔGint-104 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.750, 110.750, 77.500
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 3 / Source method: obtained synthetically / Formula: C16H17N3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
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: 2.3→55.09 Å / Num. obs: 21853 / % possible obs: 99.6 % / Redundancy: 9.7 % / Biso Wilson estimate: 56.757 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.016 / Rrim(I) all: 0.05 / Net I/σ(I): 28.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1593 / Rpim(I) all: 0.352 / Rrim(I) all: 1.155 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.302→55.086 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 17.273 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1130 5.181 %Random
Rwork0.1681 20680 --
all0.17 ---
obs0.1704 21810 99.475 %-
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: 71.803 Å2
Baniso -1Baniso -2Baniso -3
1--4.807 Å2-0 Å2-0 Å2
2---4.807 Å2-0 Å2
3---9.614 Å2
Refinement stepCycle: LAST / Resolution: 2.302→55.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 100 106 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122842
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162610
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.8333877
X-RAY DIFFRACTIONr_angle_other_deg0.5211.7415986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.402518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43610446
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.76310131
X-RAY DIFFRACTIONr_chiral_restr0.0710.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
X-RAY DIFFRACTIONr_nbd_refined0.2360.2657
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22324
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21407
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2490.212
X-RAY DIFFRACTIONr_nbd_other0.1660.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.215
X-RAY DIFFRACTIONr_mcbond_it3.1184.6521345
X-RAY DIFFRACTIONr_mcbond_other3.1094.6521345
X-RAY DIFFRACTIONr_mcangle_it4.4638.351676
X-RAY DIFFRACTIONr_mcangle_other4.4628.3521677
X-RAY DIFFRACTIONr_scbond_it4.3665.3071497
X-RAY DIFFRACTIONr_scbond_other4.3655.3091498
X-RAY DIFFRACTIONr_scangle_it6.3699.6482192
X-RAY DIFFRACTIONr_scangle_other6.3689.6492193
X-RAY DIFFRACTIONr_lrange_it8.22847.5073371
X-RAY DIFFRACTIONr_lrange_other8.22747.5133372
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
2.302-2.3620.351760.32515080.32615920.8670.81399.49750.277
2.362-2.4270.284840.31414510.31215410.870.85499.61060.271
2.427-2.4970.323910.27414240.27715200.850.89599.67110.23
2.497-2.5730.294710.24613760.24814600.9360.92999.10960.202
2.573-2.6580.236850.19913270.20114170.9510.96399.64710.166
2.658-2.7510.218650.18512940.18713690.9660.96599.26950.149
2.751-2.8540.283560.16912680.17413310.9520.97799.47410.142
2.854-2.970.238600.17212190.17612850.9610.97899.53310.147
2.97-3.1020.234530.17611830.17812390.9660.97999.75790.15
3.102-3.2530.255740.16111050.16611820.9650.98399.74620.146
3.253-3.4280.226570.17510590.17811200.9640.9899.64290.16
3.428-3.6350.242520.16710200.17110780.9670.98499.44340.158
3.635-3.8850.191470.1529670.15410160.9790.98599.80310.147
3.885-4.1950.182590.1358830.1389460.9730.98899.57720.136
4.195-4.5920.208480.1358300.1398820.9750.98899.54650.139
4.592-5.130.185560.1327400.1358000.9780.98999.50.142
5.13-5.9150.211320.1456800.1487140.9730.98699.71990.153
5.915-7.2240.204280.1645910.1666200.9830.98499.83870.172
7.224-10.1290.118250.1244630.1234960.990.99198.38710.144
10.129-55.0860.242110.2312920.2313140.9660.96596.49680.291
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)
15.49270.367-2.07622.5773-0.25732.7794-0.02370.4578-0.2499-0.41870.2230.42690.2744-0.6015-0.19930.0987-0.0854-0.10520.14120.07020.12589.175884.671516.442
24.0672-0.93160.68914.4514-2.2783.78570.04-0.4191-0.40880.3099-0.0394-0.01020.30480.2807-0.00060.1367-0.02350.01470.2920.0570.0889.93775.903139.1623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLF8 - 179
2X-RAY DIFFRACTION2ALLF184 - 350

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