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- PDB-7ni1: CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 7ni1
TitleCRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH CPD 9
Components(Myeloperoxidase) x 2
KeywordsOXIDOREDUCTASE / COMPLEX / INHIBITOR
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
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
beta-D-mannopyranose / PROTOPORPHYRIN IX CONTAINING FE / Chem-UEB / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSjogren, T. / Inghardt, T.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of AZD4831, a Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As a Potential Treatment for Heart Failure with Preserved Ejection Fraction.
Authors: Inghardt, T. / Antonsson, T. / Ericsson, C. / Hovdal, D. / Johannesson, P. / Johansson, C. / Jurva, U. / Kajanus, J. / Kull, B. / Michaelsson, E. / Pettersen, A. / Sjogren, T. / Sorensen, H. ...Authors: Inghardt, T. / Antonsson, T. / Ericsson, C. / Hovdal, D. / Johannesson, P. / Johansson, C. / Jurva, U. / Kajanus, J. / Kull, B. / Michaelsson, E. / Pettersen, A. / Sjogren, T. / Sorensen, H. / Westerlund, K. / Lindstedt, E.L.
History
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Sep 7, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Sep 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
B: Myeloperoxidase
C: Myeloperoxidase
D: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,73825
Polymers130,4174
Non-polymers5,32121
Water11,584643
1
A: Myeloperoxidase
C: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,88713
Polymers65,2092
Non-polymers2,67811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-112 kcal/mol
Surface area22770 Å2
MethodPISA
2
B: Myeloperoxidase
D: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,85112
Polymers65,2092
Non-polymers2,64310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-96 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.220, 63.820, 111.340
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Myeloperoxidase / MPO


Mass: 11974.420 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 167-271 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHILS / Cell line: HL60 / References: UniProt: P05164, myeloperoxidase
#2: Protein Myeloperoxidase / MPO


Mass: 53234.191 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 279-744 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHILS / Cell line: HL60 / References: UniProt: P05164, myeloperoxidase

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Sugars , 3 types, 8 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 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-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#9: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 656 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-UEB / (S)-1-(2-(amino(phenyl)methyl)benzyl)-2-thioxo-1,2,3,5-tetrahydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / 1-[[2-[(~{R})-azanyl(phenyl)methyl]phenyl]methyl]-2-sulfanylidene-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one


Mass: 362.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N4OS / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsRESIDUES 167 TO 270 RESIDUES 279 TO 744

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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: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG 3350, 100 MM NACL, PROTEIN BUFFER CONTAINED 50 MM AMMOIUM SULPHATE, 20 MM AMMONIUM ACETATE PH 5.5 AND 2 MM CACL
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→48.8 Å / Num. obs: 73815 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 25.16 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.089 / Rrim(I) all: 0.2 / Χ2: 0.96 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 5070 / CC1/2: 0.91 / Rpim(I) all: 0.304 / Rrim(I) all: 0.663 / Χ2: 0.91 / % possible all: 92

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDS1.1.7data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CXP

1cxp


Resolution: 2.11→46.24 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.84 / SU R Cruickshank DPI: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3581 4.85 %RANDOM
Rwork0.217 ---
obs0.219 73796 97.9 %-
Displacement parametersBiso mean: 24.09 Å2
Baniso -1Baniso -2Baniso -3
1--10.0124 Å20 Å2-2.1384 Å2
2--3.9269 Å20 Å2
3---6.0855 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.11→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9095 0 359 643 10097
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019720HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0413253HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3395SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1675HARMONIC5
X-RAY DIFFRACTIONt_it9720HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1259SEMIHARMONIC5
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_contact11886SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.12 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2647 -4.74 %
Rwork0.2473 1406 -
all0.2481 1476 -
obs--78.76 %

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