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- PDB-5qj2: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) OMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 5qj2
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) OMPLEX WITH COMPOUND-20 AKA 7-((3-(1-METHYL-1H-PYRAZOL-3- YL)BENZYL)OXY)- 1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE
Components(Myeloperoxidase) x 2
KeywordsMETAL BINDING PROTEIN / MYELOPEROXIDASE
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 / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / defense response / peroxidase activity / 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 / nucleus / metal ion binding
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-L-fucopyranose / PROTOPORPHYRIN IX CONTAINING FE / Chem-JXS / alpha-D-mannopyranose / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å
AuthorsKhan, J.A.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Potent Triazolopyridine Myeloperoxidase Inhibitors.
Authors: Wurtz, N.R. / Viet, A. / Shaw, S.A. / Dilger, A. / Valente, M.N. / Khan, J.A. / Jusuf, S. / Narayanan, R. / Fernando, G. / Lo, F. / Liu, X. / Locke, G.A. / Kopcho, L. / Abell, L.M. / Sleph, ...Authors: Wurtz, N.R. / Viet, A. / Shaw, S.A. / Dilger, A. / Valente, M.N. / Khan, J.A. / Jusuf, S. / Narayanan, R. / Fernando, G. / Lo, F. / Liu, X. / Locke, G.A. / Kopcho, L. / Abell, L.M. / Sleph, P. / Basso, M. / Zhao, L. / Wexler, R.R. / Duclos, F. / Kick, E.K.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 12, 2021Group: Structure summary / Category: chem_comp / pdbx_deposit_group
Item: _chem_comp.pdbx_synonyms / _pdbx_deposit_group.group_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
B: Myeloperoxidase
D: Myeloperoxidase
E: Myeloperoxidase
F: Myeloperoxidase
G: Myeloperoxidase
H: Myeloperoxidase
I: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,40159
Polymers261,0558
Non-polymers11,34651
Water1,13563
1
A: Myeloperoxidase
B: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,53017
Polymers65,2642
Non-polymers3,26615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-75 kcal/mol
Surface area21640 Å2
MethodPISA
2
D: Myeloperoxidase
E: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83113
Polymers65,2642
Non-polymers2,56711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-69 kcal/mol
Surface area21670 Å2
MethodPISA
3
F: Myeloperoxidase
G: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30916
Polymers65,2642
Non-polymers3,04514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14990 Å2
ΔGint-77 kcal/mol
Surface area21150 Å2
MethodPISA
4
H: Myeloperoxidase
I: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,73113
Polymers65,2642
Non-polymers2,46711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint-67 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.817, 150.949, 233.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 8 molecules ADFHBEGI

#1: Protein
Myeloperoxidase / MPO


Mass: 11974.420 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#2: Protein
Myeloperoxidase / MPO


Mass: 53289.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 4 types, 38 molecules

#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22 / 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
#4: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4 / 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
#6: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / 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
#7: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8 / 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, 76 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical ChemComp-JXS / 7-{[3-(1-methyl-1H-pyrazol-3-yl)phenyl]methoxy}-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 321.337 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H15N7O
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2010 / Details: KIRKPARTICK-BAEZ
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.82→233.1 Å / Num. obs: 61530 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 75.55 Å2 / Rsym value: 0.14 / Net I/σ(I): 9.5
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.49 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.9.6refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WDJ

5wdj


Resolution: 2.82→116.55 Å / Cor.coef. Fo:Fc: 0.9034 / Cor.coef. Fo:Fc free: 0.8538 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.408
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 3097 5.07 %RANDOM
Rwork0.2063 ---
obs0.2096 61066 99.65 %-
Displacement parametersBiso max: 137.5 Å2 / Biso mean: 58.87 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1-14.0953 Å20 Å20 Å2
2---4.7182 Å20 Å2
3----9.377 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.82→116.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17720 0 730 63 18513
Biso mean--65.58 39.1 -
Num. residues----2272
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6254SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes462HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2779HARMONIC5
X-RAY DIFFRACTIONt_it18949HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2516SEMIHARMONIC5
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_contact22816SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d18949HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg25876HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion19.95
LS refinement shellResolution: 2.82→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3462 232 5.16 %
Rwork0.2292 4260 -
all0.235 4492 -
obs--99.65 %

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