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- PDB-3wcd: The complex structure of HsSQS wtih ligand, WC-9 -

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Basic information

Entry
Database: PDB / ID: 3wcd
TitleThe complex structure of HsSQS wtih ligand, WC-9
ComponentsSqualene synthase
KeywordsTRANSFERASE / isoprenoids / drug discovery / WC-9
Function / homology
Function and homology information


farnesyl diphosphate metabolic process / squalene synthase / squalene synthase [NAD(P)H] activity / : / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression ...farnesyl diphosphate metabolic process / squalene synthase / squalene synthase [NAD(P)H] activity / : / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / metal ion binding
Similarity search - Function
Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Squalene synthase-like / Trans-isoprenyl diphosphate synthases, eukaryotic-type / Squalene and phytoene synthases signature 2. / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-(4-phenoxyphenoxy)ethyl thiocyanate / Squalene synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Huang, C.H. / Ren, F. / Zheng, Y. / Zhu, Z. / Chen, C.C. / Guo, R.T.
CitationJournal: Plos Pathog. / Year: 2014
Title: Squalene synthase as a target for Chagas disease therapeutics.
Authors: Shang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Li, J. / Zheng, Y. / Huang, C.H. / Ren, F. / Chen, C.C. / Zhu, Z. / Galizzi, M. / Li, Z.H. / Rodrigues-Poveda, C.A. / Gonzalez-Pacanowska, D. / ...Authors: Shang, N. / Li, Q. / Ko, T.P. / Chan, H.C. / Li, J. / Zheng, Y. / Huang, C.H. / Ren, F. / Chen, C.C. / Zhu, Z. / Galizzi, M. / Li, Z.H. / Rodrigues-Poveda, C.A. / Gonzalez-Pacanowska, D. / Veiga-Santos, P. / de Carvalho, T.M. / de Souza, W. / Urbina, J.A. / Wang, A.H. / Docampo, R. / Li, K. / Liu, Y.L. / Oldfield, E. / Guo, R.T.
History
DepositionMay 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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 / _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
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,81910
Polymers247,7346
Non-polymers1,0854
Water13,836768
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Squalene synthase
B: Squalene synthase
C: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4105
Polymers123,8673
Non-polymers5432
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-33 kcal/mol
Surface area38660 Å2
MethodPISA
3
D: Squalene synthase
E: Squalene synthase
F: Squalene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4105
Polymers123,8673
Non-polymers5432
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-40 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.728, 153.744, 91.431
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Squalene synthase / SQS / SS / FPP / FPP farnesyltransferase / Farnesyl-diphosphate farnesyltransferase


Mass: 41288.988 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 31-370 / Mutation: K248L, K315L, K318L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: P37268, squalene synthase
#2: Chemical
ChemComp-RWY / 2-(4-phenoxyphenoxy)ethyl thiocyanate


Mass: 271.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (FDFT_HUMAN, P37268) SHOWS CONFLICT AT THIS POSITION: D -> N

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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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.2
Details: 0.2M sodium citrate, 28% PEG 3350, pH 8.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 61519 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.7 / Num. unique all: 6087 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZF

1ezf


Resolution: 2.75→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 2941 RANDOM
Rwork0.183 --
all-61373 -
obs-58115 -
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16176 0 76 768 17020
LS refinement shellResolution: 2.75→2.85 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.262

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