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Yorodumi- PDB-8ct4: Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ct4 | ||||||||||||
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Title | Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide | ||||||||||||
Components | Dihydrolipoyl dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / flavoprotein / glycolysis / redox-active center / OXIDOREDUCTASE-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / Prevention of phagosomal-lysosomal fusion ...Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / disulfide oxidoreductase activity / pyruvate dehydrogenase complex / zymogen binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / antioxidant activity / Prevention of phagosomal-lysosomal fusion / cell redox homeostasis / flavin adenine dinucleotide binding / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å | ||||||||||||
Authors | Kochanczyk, T. / Arango, N. / Lima, C.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Not published Title: Cryo-EM structure of Mtb Lpd bound to the inhibitor 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide at 2.17 Angstrom resolution Authors: Kochanczyk, T. / Arango, N. / Michino, M. / Sun, S. / Ginn, J. / Bryk, R. / Nathan, C. / Lima, C.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ct4.cif.gz | 364 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ct4.ent.gz | 300.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ct4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ct4_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ct4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ct4_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 8ct4_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ct4 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ct4 | HTTPS FTP |
-Related structure data
Related structure data | 26981MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 49437.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: lpdC, lpd, Rv0462, MTV038.06 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHH9, dihydrolipoyl dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dihydrolipoyl dehydrogenase in complex with 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide Type: COMPLEX Details: 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide provided by the Tri-Institutional Therapeutics Discovery Institute ...Details: 2-((2-cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4-dihydro-2H-benzo[b] [1,4]oxazin-7-yl)acetamide provided by the Tri-Institutional Therapeutics Discovery Institute (tritdi.org) contact: John Ginn (jginn@tritdi.org) Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.099 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 / Details: 20 mM Tris-HCl, pH 8.0, 87.5 mM NaCl, 0.05% IGEPAL |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: Temperature 22 C, humidity 100%, Wait time 8s, Blot time: 3.5s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 70.66 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10748 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1177958 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7KMY Pdb chain-ID: AB / Accession code: 7KMY / Source name: PDB / Type: experimental model |