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Yorodumi- PDB-6lkd: in meso full-length rat KMO in complex with a pyrazoyl benzoic ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lkd | ||||||
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Title | in meso full-length rat KMO in complex with a pyrazoyl benzoic acid inhibitor | ||||||
Components | Kynurenine 3-monooxygenase | ||||||
Keywords | MEMBRANE PROTEIN / Single pass transmembrane / KMO / hydroxygenase / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information Tryptophan catabolism / L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / kynurenic acid biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity ...Tryptophan catabolism / L-kynurenine metabolic process / positive regulation of glutamate secretion, neurotransmission / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / kynurenic acid biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic process / positive regulation of glutamate secretion / cellular response to interleukin-1 / response to salt stress / FAD binding / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / extracellular space Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Mimasu, S. / Yamagishi, H. / Kiyohara, M. / Kakefuda, K. / Okuda, T. | ||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Full-length in meso structure and mechanism of rat kynurenine 3-monooxygenase inhibition. Authors: Mimasu, S. / Yamagishi, H. / Kubo, S. / Kiyohara, M. / Matsuda, T. / Yahata, T. / Thomson, H.A. / Hupp, C.D. / Liu, J. / Okuda, T. / Kakefuda, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lkd.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lkd.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lkd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6lkd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6lkd_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 6lkd_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lkd ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lkd | HTTPS FTP |
-Related structure data
Related structure data | 6lkeC 4j33S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56419.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kmo / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O88867, kynurenine 3-monooxygenase |
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-Non-polymers , 5 types, 14 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 66.67 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.04 M Tris-Cl pH 7.0, 0.06 M Bis-Tris pH 6.5, 0.3-0.51 M lithium sulfate, and 34-45 % PEG400 PH range: 6.5-7.0 / Temp details: incubated at 290 for 3 days |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.25 Å / Num. obs: 28641 / % possible obs: 99.8 % / Redundancy: 22.8 % / Biso Wilson estimate: 35.055 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.99 / Χ2: 1.22 / Net I/σ(I): 8.77 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 22.7 % / Rmerge(I) obs: 7.01 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1127 / CC1/2: 0.533 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J33 Resolution: 3→49.25 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.869 / SU B: 22.158 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.404 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.75 Å2 / Biso mean: 52.274 Å2 / Biso min: 7.87 Å2
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Refinement step | Cycle: final / Resolution: 3→49.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0
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