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- PDB-5ygi: Crystal structure of human FPPS in complex with an inhibitor THZ93 -

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Basic information

Entry
Database: PDB / ID: 5ygi
TitleCrystal structure of human FPPS in complex with an inhibitor THZ93
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / THZ93 / Complex / human FPPS / 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 / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / 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
PHOSPHATE ION / Chem-T93 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.177 Å
AuthorsLi, X.
CitationJournal: Cell / Year: 2018
Title: The Mevalonate Pathway Is a Druggable Target for Vaccine Adjuvant Discovery.
Authors: Xia, Y. / Xie, Y. / Yu, Z. / Xiao, H. / Jiang, G. / Zhou, X. / Yang, Y. / Li, X. / Zhao, M. / Li, L. / Zheng, M. / Han, S. / Zong, Z. / Meng, X. / Deng, H. / Ye, H. / Fa, Y. / Wu, H. / ...Authors: Xia, Y. / Xie, Y. / Yu, Z. / Xiao, H. / Jiang, G. / Zhou, X. / Yang, Y. / Li, X. / Zhao, M. / Li, L. / Zheng, M. / Han, S. / Zong, Z. / Meng, X. / Deng, H. / Ye, H. / Fa, Y. / Wu, H. / Oldfield, E. / Hu, X. / Liu, W. / Shi, Y. / Zhang, Y.
History
DepositionSep 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6617
Polymers40,0301
Non-polymers6316
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-46 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.743, 111.743, 66.191
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 / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 40029.691 Da / Num. of mol.: 1 / Fragment: UNP residues 72-419
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) / Strain (production host): BL21(DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-T93 / [[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid


Mass: 368.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2M Na/K phosphate, 25% glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.177→24.47 Å / Num. obs: 22270 / % possible obs: 98.9 % / Redundancy: 10.9 % / Net I/σ(I): 49.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.177→24.47 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.75
RfactorNum. reflection% reflection
Rfree0.2719 1081 4.99 %
Rwork0.2247 --
obs0.227 21651 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.177→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 36 53 2825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072825
X-RAY DIFFRACTIONf_angle_d0.833829
X-RAY DIFFRACTIONf_dihedral_angle_d15.2751687
X-RAY DIFFRACTIONf_chiral_restr0.047416
X-RAY DIFFRACTIONf_plane_restr0.005488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1765-2.27550.45831230.45632375X-RAY DIFFRACTION90
2.2755-2.39540.3871300.31462454X-RAY DIFFRACTION94
2.3954-2.54530.32491370.26222633X-RAY DIFFRACTION99
2.5453-2.74160.28731370.24972589X-RAY DIFFRACTION99
2.7416-3.01710.26951400.25372610X-RAY DIFFRACTION98
3.0171-3.45260.27451340.23192613X-RAY DIFFRACTION98
3.4526-4.34610.23881380.18732610X-RAY DIFFRACTION96
4.3461-24.74190.22991420.17892686X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -9.5248 Å / Origin y: 30.4691 Å / Origin z: -9.4937 Å
111213212223313233
T0.2234 Å2-0.0616 Å2-0.0172 Å2-0.2792 Å20.0231 Å2--0.3467 Å2
L1.9982 °2-0.2145 °20.4552 °2-2.0983 °20.5621 °2--1.854 °2
S-0.025 Å °-0.0172 Å °0.2844 Å °0.0392 Å °0.113 Å °-0.275 Å °-0.0505 Å °0.1365 Å °-0.0782 Å °
Refinement TLS groupSelection details: all

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