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- PDB-5h5r: Crystal structure of human GPX4 in complex with GXpep-2 -

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Basic information

Entry
Database: PDB / ID: 5h5r
TitleCrystal structure of human GPX4 in complex with GXpep-2
Components
  • GXpep-2
  • Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE 4 / SELENOCYSTEINE / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 12-eicosatetraenoic acid derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 12-eicosatetraenoic acid derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / arachidonate metabolic process / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / negative regulation of ferroptosis / dendrite development / protein polymerization / phospholipid metabolic process / cerebellum development / multicellular organism growth / nuclear envelope / response to estradiol / chromatin organization / spermatogenesis / response to oxidative stress / response to lipopolysaccharide / apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phospholipid hydroperoxide glutathione peroxidase GPX4
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSogabe, S. / Kadotani, A. / Lane, W. / Snell, G.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Discovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis
Authors: Sakamoto, K. / Sogabe, S. / Kamada, Y. / Matsumoto, S.I. / Kadotani, A. / Sakamoto, J.I. / Tani, A.
History
DepositionNov 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
B: GXpep-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2413
Polymers21,1492
Non-polymers921
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-1 kcal/mol
Surface area8820 Å2
Unit cell
Length a, b, c (Å)41.247, 41.247, 92.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Phospholipid hydroperoxide glutathione peroxidase, mitochondrial / PHGPx / Glutathione peroxidase 4 / GSHPx-4


Mass: 19419.070 Da / Num. of mol.: 1 / Mutation: C29S, C37A, C64S, U73C, C93R, C102S, C134E, C175V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Production host: Escherichia coli (E. coli)
References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase
#2: Protein/peptide GXpep-2


Mass: 1730.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 0.2M sodium acetate, 25% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 51699 / % possible obs: 93.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 5.7 / % possible all: 55.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBI

2obi


Resolution: 1.2→35.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.895 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16249 2558 5 %RANDOM
Rwork0.15026 ---
obs0.15087 49112 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.2→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 6 178 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191597
X-RAY DIFFRACTIONr_bond_other_d0.0110.021510
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9432162
X-RAY DIFFRACTIONr_angle_other_deg1.58933474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62223.43483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10115283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9281512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
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_it0.4650.725755
X-RAY DIFFRACTIONr_mcbond_other0.4580.724753
X-RAY DIFFRACTIONr_mcangle_it0.8031.086946
X-RAY DIFFRACTIONr_mcangle_other0.7961.086946
X-RAY DIFFRACTIONr_scbond_it0.7230.827842
X-RAY DIFFRACTIONr_scbond_other0.7190.827842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1421.2041211
X-RAY DIFFRACTIONr_long_range_B_refined3.5688.7662332
X-RAY DIFFRACTIONr_long_range_B_other3.3138.0132261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 123 -
Rwork0.162 2377 -
obs--60.68 %
Refinement TLS params.Method: refined / Origin x: 18.5175 Å / Origin y: -6.4821 Å / Origin z: 18.3799 Å
111213212223313233
T0.0124 Å20.0019 Å20.0005 Å2-0.0023 Å20.0014 Å2--0.0029 Å2
L0.4735 °20.0737 °2-0.0521 °2-0.567 °20.0733 °2--0.2684 °2
S0.0129 Å °-0.0136 Å °0.012 Å °0.0206 Å °-0.0117 Å °0.0039 Å °-0.0092 Å °-0.0047 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 197
2X-RAY DIFFRACTION1B900 - 914

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