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- PDB-9lnh: Crystal structure of Peroxiredoxin I in complex with compound LC-... -

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Basic information

Entry
Database: PDB / ID: 9lnh
TitleCrystal structure of Peroxiredoxin I in complex with compound LC-PDin20
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / Celastrol derivative / PRDX1 inhibitor
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 / fibroblast proliferation / response to oxidative stress / cell population proliferation / cadherin binding / extracellular space / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsWang, Z. / Luo, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Rapid Discovery of Celastrol Derivatives as Potent and Selective PRDX1 Inhibitors via Microplate-Based Parallel Compound Library and In Situ Screening.
Authors: Chen, S. / Wang, Z. / Gao, J. / Wang, Y. / Liang, J. / Zhu, Y. / Xu, H. / Chen, K. / Jin, L. / Zhang, H. / Xiong, H. / Luo, C.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 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)39,2253
Polymers38,6742
Non-polymers5511
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-7 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.391, 77.840, 82.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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-A1EL9 / (2~{S})-2-[[(2~{R},4~{a}~{S},6~{a}~{R},6~{a}~{S},14~{a}~{S},14~{b}~{R})-2,4~{a},6~{a},6~{a},9,14~{a}-hexamethyl-10-oxidanyl-11-oxidanylidene-1,3,4,5,6,13,14,14~{b}-octahydropicen-2-yl]carbamoylamino]butanoic acid


Mass: 550.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H46N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 8% Tacsimate pH 8.0 (v/v), 20% PEG3350 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.63→38.92 Å / Num. obs: 52208 / % possible obs: 99.89 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 12.95
Reflection shellResolution: 1.63→1.688 Å / Num. unique obs: 5163 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→38.92 Å / SU ML: 0.1707 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0796
RfactorNum. reflection% reflection
Rfree0.2023 2557 4.9 %
Rwork0.1753 49599 -
obs0.1766 52156 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.99 Å2
Refinement stepCycle: LAST / Resolution: 1.63→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 40 393 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612770
X-RAY DIFFRACTIONf_angle_d1.02273762
X-RAY DIFFRACTIONf_chiral_restr0.0613411
X-RAY DIFFRACTIONf_plane_restr0.0067484
X-RAY DIFFRACTIONf_dihedral_angle_d4.48381627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.28321440.26272719X-RAY DIFFRACTION99.83
1.66-1.70.30021340.24182717X-RAY DIFFRACTION99.79
1.7-1.730.27291450.2222709X-RAY DIFFRACTION99.76
1.73-1.770.23221370.21322734X-RAY DIFFRACTION99.97
1.77-1.820.23731370.20822701X-RAY DIFFRACTION99.82
1.82-1.870.2171280.22753X-RAY DIFFRACTION99.83
1.87-1.920.23671620.19732692X-RAY DIFFRACTION99.86
1.92-1.980.21971370.19592740X-RAY DIFFRACTION99.9
1.98-2.050.21921350.17922748X-RAY DIFFRACTION99.9
2.05-2.140.17841530.17462715X-RAY DIFFRACTION99.93
2.14-2.230.21621630.17612719X-RAY DIFFRACTION99.97
2.23-2.350.19181490.18012751X-RAY DIFFRACTION99.93
2.35-2.50.19921390.18392753X-RAY DIFFRACTION99.93
2.5-2.690.22981350.18262773X-RAY DIFFRACTION99.97
2.69-2.960.22391530.17962766X-RAY DIFFRACTION99.97
2.96-3.390.20141310.17222809X-RAY DIFFRACTION100
3.39-4.270.13951090.13922856X-RAY DIFFRACTION100
4.27-38.920.19481660.15522944X-RAY DIFFRACTION99.94

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