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- PDB-3q30: Human Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-... -

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Basic information

Entry
Database: PDB / ID: 3q30
TitleHuman Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-3-[5-(2-naphthalenyl)pentyl]aminocarbonyl-3-[5-(2-naphthalenyl)pentyloxy]propionic acid
ComponentsSqualene synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / isoprene biosynthesis / lipid synthesis / multifunctional enzyme / oxidoreductase / steroid biosynthesis / sterol biosynthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-D61 / PHOSPHATE ION / Squalene synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuzuki, M. / Shimizu, H. / Katakura, S. / Yamazaki, K. / Higashihashi, N. / Ichikawa, M. / Yokomizo, A. / Itoh, M. / Sugita, K. / Usui, H.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Discovery of a new 2-aminobenzhydrol template for highly potent squalene synthase inhibitors
Authors: Ichikawa, M. / Yokomizo, A. / Itoh, M. / Sugita, K. / Usui, H. / Shimizu, H. / Suzuki, M. / Terayama, K. / Kanda, A.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 1, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9105
Polymers39,1671
Non-polymers7434
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.973, 59.526, 84.139
Angle α, β, γ (deg.)90.00, 115.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39166.699 Da / Num. of mol.: 1 / Fragment: UNP residues 31-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P37268, squalene synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-D61 / (2R,3R)-2-(carboxymethoxy)-4-{[5-(naphthalen-2-yl)pentyl]amino}-3-{[5-(naphthalen-2-yl)pentyl]oxy}-4-oxobutanoic acid


Mass: 599.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H41NO7
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: seeding method, pH 5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 19, 2000 / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 25771 / Num. obs: 25771 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.59 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3 / Num. unique all: 2567 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZF

1ezf


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.015 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Although electron density peak corresponding to Arg52-Phe54 exist, this peptide region cannot be modeled to the shape of observed density. Possible cause of this failure is multiple ...Details: Although electron density peak corresponding to Arg52-Phe54 exist, this peptide region cannot be modeled to the shape of observed density. Possible cause of this failure is multiple conformation. There is a planer electron density peak possibly corresponding to the intrinsic lipid molecule between bound compound and Phe 54. Any atomic model for this density has not neen built.
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1235 4.8 %RANDOM
Rwork0.20686 ---
all0.20833 25763 --
obs0.20833 24528 100 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 29.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-1.81 Å2
2--0 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 51 264 2943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222739
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9713708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71624.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0261516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9531.51647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6272.52665
X-RAY DIFFRACTIONr_scbond_it1.58121092
X-RAY DIFFRACTIONr_scangle_it2.37931043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.325 115 -
Rwork0.243 2390 -
obs--100 %

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