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- PDB-4mmm: Human Pdrx5 complex with a ligand BP7 -

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Basic information

Entry
Database: PDB / ID: 4mmm
TitleHuman Pdrx5 complex with a ligand BP7
ComponentsPeroxiredoxin-5, mitochondrial
KeywordsOXIDOREDUCTASE / enzyme
Function / homology
Function and homology information


peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species / antioxidant activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to reactive oxygen species / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,1'-BIPHENYL-3,4-DIOL / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsGuichou, J.F.
CitationJournal: Plos One / Year: 2014
Title: Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5
Authors: Aguirre, C. / Brink, T.T. / Guichou, J.F. / Cala, O. / Krimm, I.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Peroxiredoxin-5, mitochondrial
C: Peroxiredoxin-5, mitochondrial
E: Peroxiredoxin-5, mitochondrial
G: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7146
Polymers71,3424
Non-polymers3722
Water15,511861
1
A: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0222
Polymers17,8351
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0222
Polymers17,8351
Non-polymers1861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Peroxiredoxin-5, mitochondrial


Theoretical massNumber of molelcules
Total (without water)17,8351
Polymers17,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Peroxiredoxin-5, mitochondrial


Theoretical massNumber of molelcules
Total (without water)17,8351
Polymers17,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Peroxiredoxin-5, mitochondrial
E: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8573
Polymers35,6712
Non-polymers1861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area13230 Å2
MethodPISA
6
C: Peroxiredoxin-5, mitochondrial
G: Peroxiredoxin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8573
Polymers35,6712
Non-polymers1861
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.467, 101.228, 58.754
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin-5, mitochondrial / Alu corepressor 1 / Antioxidant enzyme B166 / AOEB166 / Liver tissue 2D-page spot 71B / PLP / ...Alu corepressor 1 / Antioxidant enzyme B166 / AOEB166 / Liver tissue 2D-page spot 71B / PLP / Peroxiredoxin V / Prx-V / Peroxisomal antioxidant enzyme / TPx type VI / Thioredoxin peroxidase PMP20 / Thioredoxin reductase


Mass: 17835.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX5, ACR1, SBBI10 / Production host: Escherichia coli (E. coli) / References: UniProt: P30044, peroxiredoxin
#2: Chemical ChemComp-BP7 / 1,1'-BIPHENYL-3,4-DIOL / 3,4-DIHYDROXYBIPHENYL


Mass: 186.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 22% PEG3350, 0.1M sodium citrate buffer (pH 5.3), 0.2M potassium sodium tartrate, 5mM 1,4-dithio-dl-threitol, 0.02%(w/v) sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07244 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07244 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.48
11-h,-k,l20.52
ReflectionResolution: 1.47→44.05 Å / Num. obs: 119074 / % possible obs: 99.8 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.1

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Processing

Software
NameVersionClassification
DNAdata collection
X-PLORmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→44.05 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.708 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19155 6420 5.1 %RANDOM
Rwork0.16236 ---
obs0.16383 119074 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20.72 Å2
2--8.17 Å20 Å2
3----7.41 Å2
Refinement stepCycle: LAST / Resolution: 1.47→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 28 861 5673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195010
X-RAY DIFFRACTIONr_bond_other_d0.0010.025016
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9936796
X-RAY DIFFRACTIONr_angle_other_deg0.7623.00111594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22125.055182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1531521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021047
X-RAY DIFFRACTIONr_mcbond_it0.5991.2642636
X-RAY DIFFRACTIONr_mcbond_other0.5981.2642635
X-RAY DIFFRACTIONr_mcangle_it0.9911.8923303
X-RAY DIFFRACTIONr_mcangle_other0.9911.8933304
X-RAY DIFFRACTIONr_scbond_it0.751.3512374
X-RAY DIFFRACTIONr_scbond_other0.751.3512375
X-RAY DIFFRACTIONr_scangle_other1.21.9943485
X-RAY DIFFRACTIONr_long_range_B_refined3.74511.3216345
X-RAY DIFFRACTIONr_long_range_B_other3.74511.3236346
LS refinement shellResolution: 1.47→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 462 -
Rwork0.213 8096 -
obs--87.39 %

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