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- PDB-6wy0: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Entry
Database: PDB / ID: 6wy0
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-40 A.K.A 7-[(1R)-1-phenyl-3-{[(1r,4r)-4-phenylcyclohexyl]amino}propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
Components(Myeloperoxidase ...) x 2
KeywordsOXIDOREDUCTASE / MYELOPEROXIDASE / MPO / HEME
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-UFA / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 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 1.2Nov 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
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)272,21140
Polymers261,1838
Non-polymers11,02832
Water2,684149
1
A: Myeloperoxidase light chain
B: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95110
Polymers65,2962
Non-polymers2,6558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-85 kcal/mol
Surface area21930 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,19011
Polymers65,2962
Non-polymers2,8949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-94 kcal/mol
Surface area22150 Å2
MethodPISA
3
F: Myeloperoxidase light chain
G: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,15410
Polymers65,2962
Non-polymers2,8598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-84 kcal/mol
Surface area22070 Å2
MethodPISA
4
H: Myeloperoxidase light chain
I: Myeloperoxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9169
Polymers65,2962
Non-polymers2,6207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-73 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.348, 151.402, 229.728
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) / References: UniProt: P05164, myeloperoxidase
#2: Protein
Myeloperoxidase heavy chain / MPO


Mass: 53321.270 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 , 3 types, 12 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.: 4
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
#4: 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-Glycam 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
[]{[(4+1)][b-D-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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, 169 molecules

#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#7: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-UFA / 7-{(1R)-1-phenyl-3-[(trans-4-phenylcyclohexyl)amino]propyl}-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 426.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H30N6 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
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: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→47.69 Å / Num. obs: 62583 / % possible obs: 100 % / Redundancy: 6.7 % / Rsym value: 0.097 / Net I/σ(I): 14.2
Reflection shellResolution: 2.799→2.82 Å / Num. unique obs: 1251 / CC1/2: 0.01

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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: 2.799→47.69 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 3170 5.07 %RANDOM
Rwork0.1846 ---
obs0.1862 62543 99.9 %-
Displacement parametersBiso max: 108.9 Å2 / Biso mean: 55.74 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å20 Å20 Å2
2---8.2949 Å20 Å2
3---3.9249 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.799→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17864 0 731 149 18744
Biso mean--56.01 42.18 -
Num. residues----2272
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6554SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3343HARMONIC5
X-RAY DIFFRACTIONt_it19112HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2533SEMIHARMONIC5
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_contact15165SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19112HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg26111HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion16.84
LS refinement shellResolution: 2.8→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2415 60 4.8 %
Rwork0.2294 1191 -
all0.2299 1251 -
obs--99.92 %
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)
11.27980.2160.82191.97610.29332.2708-0.0562-0.1322-0.06540.0268-0.19710.20540.0488-0.46030.2533-0.1686-0.04620.1451-0.0853-0.1336-0.055140.80421.847822.8388
21.23390.21410.3041.23840.35261.9180.0448-0.1459-0.32680.121-0.19630.28940.3556-0.550.1515-0.1924-0.16120.1569-0.1084-0.1157-0.0259135.1512.992525.4094
30.2013-0.51440.03370.5223-0.1730-0.08010.19920.0671-0.03060.02220.0669-0.0762-0.13760.05790.07020.02530.0126-0.07860.0452-0.0153126.56958.451829.2063
41.71510.43810.19761.95570.89212.1447-0.0326-0.0646-0.05280.02810.0624-0.0226-0.2257-0.0608-0.0298-0.0602-0.05970.0663-0.1844-0.0218-0.1421164.65939.932739.3637
51.09730.20750.05671.29430.80111.8399-0.10170.08380.0806-0.19450.1874-0.2022-0.45580.3253-0.0857-0.0348-0.1470.061-0.1454-0.0413-0.1318173.09146.091335.9106
61.16390.23380.8151.48160.02841.46690.06010.0748-0.012-0.0809-0.03230.1606-0.02160.0456-0.0278-0.11170.0626-0.0632-0.0476-0.0206-0.1145105.40956.027318.3
71.00310.13870.31131.0426-0.06141.1840.10740.0745-0.1952-0.0409-0.04580.23360.2044-0.1517-0.0616-0.0863-0.0144-0.0883-0.1028-0.0468-0.055298.643447.968321.7064
81.694-0.2928-0.37561.75350.0942.2427-0.05360.13030.11770.0643-0.062-0.1538-0.10210.03420.1156-0.1191-0.0149-0.1066-0.15950.0785-0.0744124.42878.719835.544
91.3195-0.09410.04781.02710.19391.1958-0.06310.19640.3050.00820.0073-0.299-0.27970.27460.0558-0.1302-0.0793-0.1123-0.10560.1005-0.0204133.76283.788233.253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 103
2X-RAY DIFFRACTION2{ B|* }B114 - 577
3X-RAY DIFFRACTION3{ Q|* }Q1 - 4
4X-RAY DIFFRACTION4{ D|* }D1 - 104
5X-RAY DIFFRACTION5{ E|* }E113 - 577
6X-RAY DIFFRACTION6{ F|* }F1 - 104
7X-RAY DIFFRACTION7{ G|* }G114 - 577
8X-RAY DIFFRACTION8{ H|* }H1 - 103
9X-RAY DIFFRACTION9{ I|* }I113 - 577

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