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- PDB-9ve2: Crystal Structure of Human Peroxiredoxin I in Complex with Fluvastatin -

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Basic information

Entry
Database: PDB / ID: 9ve2
TitleCrystal Structure of Human Peroxiredoxin I in Complex with Fluvastatin
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / PRDX1 / Complex / Fluvastatin
Function / homology
Function and homology information


leukocyte activation / Scavenging by Class B Receptors / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / removal of superoxide radicals / cell redox homeostasis ...leukocyte activation / Scavenging by Class B Receptors / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / removal of superoxide radicals / cell redox homeostasis / skeletal system development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cell population proliferation / melanosome / response to oxidative stress / cadherin binding / : / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chem-115 / Peroxiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, H. / Xu, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22ZR1474200 China
CitationJournal: To Be Published
Title: Fluvastatin protects Leydig cells in orchitis through direct activation of Peroxiredoxin 1
Authors: Zhang, H. / Xu, H.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0863
Polymers38,6742
Non-polymers4111
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.833, 78.097, 81.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peroxiredoxin-1 / Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / ...Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Thioredoxin-dependent peroxiredoxin 1


Mass: 19337.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06830, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-115 / (3R,5S,6E)-7-[3-(4-fluorophenyl)-1-(propan-2-yl)-1H-indol-2-yl]-3,5-dihydroxyhept-6-enoic acid / FLUVASTATIN


Mass: 411.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26FNO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate 0.1 M Cacodylate pH 6.5 18% PEG 8000, as 10% v/v Tacsimate pH 7.5, 0.1M MES pH 6.5, and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→42.59 Å / Num. obs: 39083 / % possible obs: 99.59 % / Redundancy: 13.2 % / Biso Wilson estimate: 16.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08628 / Net I/σ(I): 30.77
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3855 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.59 Å / SU ML: 0.1822 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1922 1926 4.94 %
Rwork0.1548 37092 -
obs0.1566 39018 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 30 484 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062735
X-RAY DIFFRACTIONf_angle_d0.8463703
X-RAY DIFFRACTIONf_chiral_restr0.0613401
X-RAY DIFFRACTIONf_plane_restr0.0069481
X-RAY DIFFRACTIONf_dihedral_angle_d10.8491610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.23561260.19312605X-RAY DIFFRACTION99.93
1.84-1.890.21971370.17022621X-RAY DIFFRACTION100
1.89-1.950.22271290.17892620X-RAY DIFFRACTION99.1
1.95-2.010.21551260.15762627X-RAY DIFFRACTION100
2.01-2.090.20531420.15462624X-RAY DIFFRACTION99.96
2.09-2.170.19291290.15642652X-RAY DIFFRACTION100
2.17-2.270.20261470.1622606X-RAY DIFFRACTION99.85
2.27-2.390.20321230.15912636X-RAY DIFFRACTION99.89
2.39-2.540.20131630.15722629X-RAY DIFFRACTION100
2.54-2.730.22611430.17512627X-RAY DIFFRACTION98.68
2.73-3.010.19291530.16162623X-RAY DIFFRACTION98.79
3.01-3.440.19771400.15152684X-RAY DIFFRACTION99.89
3.44-4.340.15971240.12932727X-RAY DIFFRACTION99.58
4.34-42.590.15391440.14672811X-RAY DIFFRACTION98.9

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