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Yorodumi- PDB-7ni1: CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ni1 | ||||||
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Title | CRYSTAL STRUCTURE OF NATIVE HUMAN MYELOPEROXIDASE IN COMPLEX WITH CPD 9 | ||||||
Components | (Myeloperoxidase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Sjogren, T. / Inghardt, T. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ni1.cif.gz | 263.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ni1.ent.gz | 208.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ni1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ni1_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7ni1_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7ni1_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 7ni1_validation.cif.gz | 70.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/7ni1 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/7ni1 | HTTPS FTP |
-Related structure data
Related structure data | 7ni3C 1cxpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | 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 | 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 | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / #9: Sugar | |
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-Non-polymers , 5 types, 656 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #8: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | RESIDUES 167 TO 270 RESIDUES 279 TO 744 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 24.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→46.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.12 Å / Total num. of bins used: 50
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