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

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Basic information

Entry
Database: PDB / ID: 7lan
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-30 AKA 7-[(3~{S},4~{R},6~{R})-4-benzyl-2-oxa-7,13,14-triazatetracyclo[14.3.1.1^{3,6}.1^{11,14}]docosa-1(19),11(21),12,16(20),17-pentaen-10-yl]-3~{H}-triazolo[4,5-b]pyridin-5-amine
Components
  • Isoform H14 of Myeloperoxidase
  • Myeloperoxidase light chain
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 / hydrogen peroxide catabolic process / secretory granule / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-XS1 / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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

Downloads & links

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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
F: Myeloperoxidase light chain
G: Isoform H14 of Myeloperoxidase
H: Myeloperoxidase light chain
I: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,22836
Polymers260,7708
Non-polymers11,45828
Water17,402966
1
A: Myeloperoxidase light chain
B: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14310
Polymers65,1932
Non-polymers2,9518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-84 kcal/mol
Surface area21870 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0728
Polymers65,1932
Non-polymers2,8806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-63 kcal/mol
Surface area22310 Å2
MethodPISA
3
F: Myeloperoxidase light chain
G: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,14310
Polymers65,1932
Non-polymers2,9518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-83 kcal/mol
Surface area22130 Å2
MethodPISA
4
H: Myeloperoxidase light chain
I: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8698
Polymers65,1932
Non-polymers2,6776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-65 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.211, 150.388, 231.006
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 light chain / / MPO


Mass: 11974.420 Da / Num. of mol.: 4 / 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.: 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 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.: 3
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
#4: 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-ROHGlycam 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
[][D-1-deoxy-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
#7: 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.: 5 / 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

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Non-polymers , 5 types, 982 molecules

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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-XS1 / 7-[(3R,4S,6S,10R)-4-benzyl-2-oxa-7,13,14-triazatetracyclo[14.3.1.1~3,6~.1~11,14~]docosa-1(20),11(21),12,16,18-pentaen-10-yl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 520.628 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H32N8O / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 966 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 114459 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.8 / Net I/σ(I): 18.7
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 11351

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WY7

6wy7


Resolution: 2.28→47.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9253 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.343 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 5696 5 %RANDOM
Rwork0.2003 ---
obs0.2022 113977 99.96 %-
Displacement parametersBiso max: 117.94 Å2 / Biso mean: 44.53 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.472 Å20 Å20 Å2
2--0.3916 Å20 Å2
3----5.8636 Å2
Refine analyzeLuzzati coordinate error obs: 0.293 Å
Refinement stepCycle: final / Resolution: 2.28→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17871 0 768 966 19605
Biso mean--47.35 45.48 -
Num. residues----2270
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6601SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes457HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2976HARMONIC5
X-RAY DIFFRACTIONt_it19293HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2552SEMIHARMONIC5
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_contact23028SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19293HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg26479HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion16.09
LS refinement shellResolution: 2.28→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2904 394 4.73 %
Rwork0.2415 7944 -
all0.2439 8338 -
obs--99.96 %

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