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- PDB-6wyd: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Entry
Database: PDB / ID: 6wyd
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid
Components(Myeloperoxidase ...) x 2
KeywordsOXIDOREDUCTASE / 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 / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / chromatin binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding
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
7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine / beta-D-mannopyranose / alpha-L-fucopyranose / HEME C / alpha-D-mannopyranose / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKhan, J.A.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Discovery and structure activity relationships of 7-benzyl triazolopyridines as stable, selective, and reversible inhibitors of myeloperoxidase.
Authors: Shaw, S.A. / Vokits, B.P. / Dilger, A.K. / Viet, A. / Clark, C.G. / Abell, L.M. / Locke, G.A. / Duke, G. / Kopcho, L.M. / Dongre, A. / Gao, J. / Krishnakumar, A. / Jusuf, S. / Khan, J. / ...Authors: Shaw, S.A. / Vokits, B.P. / Dilger, A.K. / Viet, A. / Clark, C.G. / Abell, L.M. / Locke, G.A. / Duke, G. / Kopcho, L.M. / Dongre, A. / Gao, J. / Krishnakumar, A. / Jusuf, S. / Khan, J. / Spronk, S.A. / Basso, M.D. / Zhao, L. / Cantor, G.H. / Onorato, J.M. / Wexler, R.R. / Duclos, F. / Kick, E.K.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)271,95963
Polymers261,1198
Non-polymers10,84055
Water4,684260
1
A: Myeloperoxidase light chain
B: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04516
Polymers65,2802
Non-polymers2,76514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-105 kcal/mol
Surface area21710 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04516
Polymers65,2802
Non-polymers2,76514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-102 kcal/mol
Surface area22620 Å2
MethodPISA
3
F: Myeloperoxidase light chain
G: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,82415
Polymers65,2802
Non-polymers2,54413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-98 kcal/mol
Surface area22960 Å2
MethodPISA
4
H: Myeloperoxidase light chain
I: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04516
Polymers65,2802
Non-polymers2,76514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-102 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.683, 150.651, 231.060
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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Myeloperoxidase ... , 2 types, 8 molecules ADFHBEGI

#1: Protein
Myeloperoxidase light chain / MPO


Mass: 11974.420 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Blood Neutrophill / References: UniProt: P05164, myeloperoxidase
#2: Protein
Myeloperoxidase heavy chain / MPO


Mass: 53305.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 4 types, 35 molecules

#4: 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.: 19
Source method: isolated from a genetically manipulated source
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
#5: 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: isolated from a genetically manipulated source
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
#7: 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: isolated from a genetically manipulated source
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
#8: 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: isolated from a genetically manipulated source
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, 280 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Chemical
ChemComp-7GD / 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 225.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H11N5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.64 %
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: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→200 Å / Num. obs: 82041 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.29 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.7
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 7 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5972 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.6refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QJ2

6qj2


Resolution: 2.55→115.53 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.8939 / SU R Cruickshank DPI: 0.824 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.732 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 4084 5 %RANDOM
Rwork0.1935 ---
obs0.1965 81612 99.95 %-
Displacement parametersBiso max: 128.16 Å2 / Biso mean: 50.55 Å2 / Biso min: 13.98 Å2
Baniso -1Baniso -2Baniso -3
1-6.4398 Å20 Å20 Å2
2---0.5081 Å20 Å2
3----5.9317 Å2
Refine analyzeLuzzati coordinate error obs: 0.322 Å
Refinement stepCycle: final / Resolution: 2.55→115.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17784 0 690 260 18734
Biso mean--54.64 40.32 -
Num. residues----2272
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6290SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes463HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2773HARMONIC5
X-RAY DIFFRACTIONt_it18939HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2504SEMIHARMONIC5
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_contact22899SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d18939HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg25843HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion18.4
LS refinement shellResolution: 2.55→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3291 264 4.42 %
Rwork0.2351 5708 -
all0.2391 5972 -
obs--99.95 %

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