[English] 日本語
![](img/lk-miru.gif)
- EMDB-26981: Cryo-EM structure of Mtb Lpd bound to inhibitor complex with 2-((... -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | ||||||||||||
![]() | Density-modified map generated using phenix.cryoem.resolve | ||||||||||||
![]() |
| ||||||||||||
![]() | flavoprotein / glycolysis / redox-active center / OXIDOREDUCTASE-INHIBITOR complex | ||||||||||||
Function / homology | ![]() Cell redox homeostasis / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / NADH binding / pyruvate dehydrogenase complex / disulfide oxidoreductase activity / 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 / pyruvate dehydrogenase complex / disulfide oxidoreductase activity / 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 | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.17 Å | ||||||||||||
![]() | Kochanczyk T / Arango N / Lima CD | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 CD | ||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 3.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 21 KB 21 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 76.3 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 109.6 MB 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 751.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 751.2 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ct4MC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density-modified map generated using phenix.cryoem.resolve | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Raw map
File | emd_26981_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Raw map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half-map 1
File | emd_26981_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half-map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half-map 2
File | emd_26981_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half-map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Dihydrolipoyl dehydrogenase in complex with 2-((2-cyano-N,5-dimet...
Entire | 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 |
---|---|
Components |
|
-Supramolecule #1: Dihydrolipoyl dehydrogenase in complex with 2-((2-cyano-N,5-dimet...
Supramolecule | 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 / ID: 1 / Parent: 0 / Macromolecule list: #1 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) |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 99 KDa |
-Macromolecule #1: Dihydrolipoyl dehydrogenase
Macromolecule | Name: Dihydrolipoyl dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: dihydrolipoyl dehydrogenase |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.437035 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSMTHYDVVV LGAGPGGYVA AIRAAQLGLS TAIVEPKYWG GVCLNVGCIP SKALLRNAEL VHIFTKDAKA FGISGEVTFD YGIAYDRSR KVAEGRVAGV HFLMKKNKIT EIHGYGTFAD ANTLLVDLND GGTESVTFDN AIIATGSSTR LVPGTSLSAN V VTYEEQIL ...String: GSMTHYDVVV LGAGPGGYVA AIRAAQLGLS TAIVEPKYWG GVCLNVGCIP SKALLRNAEL VHIFTKDAKA FGISGEVTFD YGIAYDRSR KVAEGRVAGV HFLMKKNKIT EIHGYGTFAD ANTLLVDLND GGTESVTFDN AIIATGSSTR LVPGTSLSAN V VTYEEQIL SRELPKSIII AGAGAIGMEF GYVLKNYGVD VTIVEFLPRA LPNEDADVSK EIEKQFKKLG VTILTATKVE SI ADGGSQV TVTVTKDGVA QELKAEKVLQ AIGFAPNVEG YGLDKAGVAL TDRKAIGVDD YMRTNVGHIY AIGDVNGLLQ LAH VAEAQG VVAAETIAGA ETLTLGDHRM LPRATFCQPN VASFGLTEQQ ARNEGYDVVV AKFPFTANAK AHGVGDPSGF VKLV ADAKH GELLGGHLVG HDVAELLPEL TLAQRWDLTA SELARNVHTH PTMSEALQEC FHGLVGHMIN F UniProtKB: Dihydrolipoyl dehydrogenase |
-Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD |
---|---|
Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ![]() ChemComp-FAD: |
-Macromolecule #3: N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(ox...
Macromolecule | Name: N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide type: ligand / ID: 3 / Number of copies: 2 / Formula: OU6 |
---|---|
Molecular weight | Theoretical: 495.551 Da |
Chemical component information | ![]() ChemComp-OU6: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 665 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3 mg/mL |
---|---|
Buffer | pH: 8 / Details: 20 mM Tris-HCl, pH 8.0, 87.5 mM NaCl, 0.05% IGEPAL |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: Temperature 22 C, humidity 100%, Wait time 8s, Blot time: 3.5s. |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 10748 / Average exposure time: 4.0 sec. / Average electron dose: 70.66 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: AB / Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Software | Name: PHENIX (ver. 1.20.1-44487) |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
Output model | ![]() PDB-8ct4: |