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- PDB-6wy7: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 6wy7
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-41 A.K.A 7-[1-phenyl-3-({4-phenylbicyclo[2.2.2]octan-1-yl}amino)propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
Components(Myeloperoxidase ...) x 2
KeywordsOXIDOREDUCTASE / MYELOPEROXIDASE / MPO
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 / 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
: / 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
HEME C / Chem-UFD / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 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: 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 1.2Nov 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: Myeloperoxidase light chain
B: Myeloperoxidase heavy chain
D: Myeloperoxidase light chain
E: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,69818
Polymers130,5914
Non-polymers5,10614
Water17,096949
1
A: Myeloperoxidase light chain
B: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,97710
Polymers65,2962
Non-polymers2,6818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-85 kcal/mol
Surface area22390 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7208
Polymers65,2962
Non-polymers2,4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-75 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.998, 104.998, 223.998
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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Myeloperoxidase ... , 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 / Source: (natural) Homo sapiens (human) / Cell: Blood Neutrophill / References: UniProt: P05164, myeloperoxidase
#2: Protein Myeloperoxidase heavy chain / MPO


Mass: 53321.270 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 , 2 types, 5 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 958 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-UFD / 7-{(1R)-1-phenyl-3-[(4-phenylbicyclo[2.2.2]octan-1-yl)amino]propyl}-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 452.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32N6 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
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: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.0089→46.96 Å / Num. obs: 75062 / % possible obs: 100 % / Redundancy: 12.9 % / Rsym value: 0.123 / Net I/σ(I): 18.9
Reflection shellResolution: 2.089→2.1 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 1500

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (17-DEC-2019)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5QJ2

5qj2


Resolution: 2.089→46.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 3777 5.04 %RANDOM
Rwork0.1585 ---
obs0.1599 74964 100 %-
Displacement parametersBiso max: 72.28 Å2 / Biso mean: 24.38 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-5.4182 Å20 Å20 Å2
2--5.4182 Å20 Å2
3----10.8363 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 2.089→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9036 0 343 949 10328
Biso mean--25.38 32.31 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3354SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1689HARMONIC5
X-RAY DIFFRACTIONt_it9639HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1256SEMIHARMONIC5
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_contact9443SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9639HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg13153HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion14.96
LS refinement shellResolution: 2.09→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.1831 84 5.6 %
Rwork0.1734 1416 -
all0.1739 1500 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5136-0.0109-0.00540.8321-0.09210.49290.00470.02390.03520.0018-0.02770.0509-0.0323-0.02430.023-0.0394-0.0091-0.0176-0.066-0.0097-0.0399-15.4184-42.432418.4828
20.32040.01420.02240.6763-0.02720.4740.00360.0001-0.03740.0331-0.0120.00470.0678-0.03530.0084-0.0219-0.0046-0.0102-0.0537-0.0089-0.0312-14.1982-52.709622.096
30.62690.0556-0.18290.619-0.17410.6186-0.0038-0.0099-0.0272-0.0224-0.02370.03550.0144-0.04090.0275-0.03380.0131-0.0224-0.06840.003-0.0291-18.7215-12.281533.9187
40.35870.026-0.12350.5372-0.06650.39340.01220.01390.0414-0.0349-0.0018-0.0101-0.0711-0.0254-0.0103-0.01380.0062-0.0259-0.06-0.0006-0.034-15.9198-2.13731.0644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 103
2X-RAY DIFFRACTION2{ B|* }B113 - 577
3X-RAY DIFFRACTION3{ D|* }D1 - 103
4X-RAY DIFFRACTION4{ E|* }E114 - 577

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