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- PDB-9dex: Crystal structure of human peroxiredoxin 1 in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 9dex
TitleCrystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / human peroxiredoxin 1 / covalent inhibitor complex
Function / homology
Function and homology information


leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / natural killer cell mediated cytotoxicity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of stress-activated MAPK cascade / natural killer cell mediated cytotoxicity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / skeletal system development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / melanosome / response to oxidative stress / fibroblast proliferation / cell population proliferation / cadherin binding / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
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
: / DI(HYDROXYETHYL)ETHER / Peroxiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLowther, W.T. / Gumpena, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097
Authors: Lowther, W.T. / Gumpena, R.
History
DepositionAug 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,93226
Polymers43,9202
Non-polymers2,01224
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-25 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.315, 78.799, 83.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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: 21959.957 Da / Num. of mol.: 2 / Mutation: C71S, C83S, C173S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06830, thioredoxin-dependent peroxiredoxin

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Non-polymers , 5 types, 223 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-IY4 / methyl N-(2-{[(2M)-2-(pyridin-3-yl)-1,3-thiazole-4-carbonyl]amino}prop-2-enoyl)-D-alaninate


Mass: 360.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H16N4O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES pH 7.3, 1.8 M Ammonium Sulfate, 2% (v/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 14, 2020
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20042 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.066 / Rrim(I) all: 0.155 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 844 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.35 / Rrim(I) all: 0.664

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.122 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19236 881 4.4 %RANDOM
Rwork0.16187 ---
obs0.16325 19084 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2---0.72 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.3→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 127 199 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122790
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162598
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6583737
X-RAY DIFFRACTIONr_angle_other_deg0.6631.576044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.6481012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22710447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
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_it1.8132.3141332
X-RAY DIFFRACTIONr_mcbond_other1.7752.3141332
X-RAY DIFFRACTIONr_mcangle_it2.6613.461662
X-RAY DIFFRACTIONr_mcangle_other2.6613.4621663
X-RAY DIFFRACTIONr_scbond_it3.0482.7611458
X-RAY DIFFRACTIONr_scbond_other3.0472.7641459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5963.9262075
X-RAY DIFFRACTIONr_long_range_B_refined6.14931.9883029
X-RAY DIFFRACTIONr_long_range_B_other6.14131.9773018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 61 -
Rwork0.223 1264 -
obs--91.13 %

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