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- PDB-6j0o: Crystal structure of CERT START domain in complex with compound SC1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j0o | ||||||
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Title | Crystal structure of CERT START domain in complex with compound SC1 | ||||||
![]() | LIPID-TRANSFER PROTEIN CERT | ||||||
![]() | LIPID TRANSPORT / CERT / PH / START / COMPLEX | ||||||
Function / homology | ![]() intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / response to endoplasmic reticulum stress / mitochondrion organization / muscle contraction / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K. | ||||||
![]() | ![]() Title: Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT Authors: Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Suzuki, M. / Kobayashi, S. / Hanada, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.4 KB | Display | ![]() |
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Full document | ![]() | 778 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zygC ![]() 5zyhC ![]() 5zyiC ![]() 5zyjC ![]() 5zykC ![]() 5zylC ![]() 5zymC ![]() 6iezC ![]() 6if0C ![]() 6j81C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27056.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-XAF / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | UNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. ...UNX 601 was modeled on an electron density peak clearly observed near methylpyridine moiety of XAF. However distances between this peak and surrounding H-bond donor/acceptor are too short. Therefore it is assigned to unknown atom, not to water oxygen. |
Sequence details | Authors state that these amino residues are originated from protease site after N-terminal affinity tag. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.1M trisodium citrate/HCL buffer, pH5.9 containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 10, 2014 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30.13 Å / Num. obs: 27078 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 16.4 / Num. measured all: 122989 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.37 Å2 / Biso mean: 26.48 Å2 / Biso min: 13.38 Å2
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Refinement step | Cycle: final / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.863 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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