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- PDB-7lae: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 7lae
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-4
Components
  • Isoform H14 of Myeloperoxidase
  • Myeloperoxidase light chain
KeywordsOXIDOREDUCTASE / Myeloperoxidase / MPO / HEME-DEPENDENT PEROXIDASE
Function / homology
Function and homology information


myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule / removal of superoxide radicals / defense response to fungus / response to mechanical stimulus / peroxidase activity / hydrogen peroxide catabolic process / secretory granule / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-L-fucopyranose / PROTOPORPHYRIN IX CONTAINING FE / alpha-D-mannopyranose / Chem-XRV / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsKhan, J.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Small molecule and macrocyclic pyrazole derived inhibitors of myeloperoxidase (MPO).
Authors: Hu, C.H. / Neissel Valente, M.W. / Halpern, O.S. / Jusuf, S. / Khan, J.A. / Locke, G.A. / Duke, G.J. / Liu, X. / Duclos, F.J. / Wexler, R.R. / Kick, E.K. / Smallheer, J.M.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloperoxidase light chain
B: Isoform H14 of Myeloperoxidase
D: Myeloperoxidase light chain
E: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,97328
Polymers130,3854
Non-polymers5,58824
Water724
1
A: Myeloperoxidase light chain
B: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,02215
Polymers65,1932
Non-polymers2,82913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-91 kcal/mol
Surface area21860 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95113
Polymers65,1932
Non-polymers2,75911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-70 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.917, 106.917, 238.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Myeloperoxidase light chain / / MPO


Mass: 11974.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Blood Neutrophill / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#2: Protein Isoform H14 of Myeloperoxidase / MPO


Mass: 53218.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 5 types, 16 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 12 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-XRV / 7-{[1-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 309.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12FN7 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
PH range: 7.5?

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→48.8 Å / Num. obs: 29502 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.6
Reflection shellResolution: 2.97→3.13 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WY7

6wy7


Resolution: 2.97→37.28 Å / Cor.coef. Fo:Fc: 0.9025 / Cor.coef. Fo:Fc free: 0.8463 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.435
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1496 5.09 %RANDOM
Rwork0.2164 ---
obs0.2189 29416 100 %-
Displacement parametersBiso max: 149.23 Å2 / Biso mean: 68.24 Å2 / Biso min: 21.16 Å2
Baniso -1Baniso -2Baniso -3
1--10.9043 Å20 Å20 Å2
2---10.9043 Å20 Å2
3---21.8087 Å2
Refine analyzeLuzzati coordinate error obs: 0.403 Å
Refinement stepCycle: final / Resolution: 2.97→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8783 0 362 4 9149
Biso mean--80.07 41.98 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3165SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes212HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1438HARMONIC5
X-RAY DIFFRACTIONt_it9388HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11113SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9388HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12831HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion18.25
LS refinement shellResolution: 2.97→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3398 164 5.83 %
Rwork0.2392 2651 -
all0.2448 2815 -
obs--100 %

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