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- PDB-8d24: Crystal structure of Plasmodium falciparum GRP78-NBD in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d24 | ||||||
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Title | Crystal structure of Plasmodium falciparum GRP78-NBD in complex with VER155008 | ||||||
![]() | Chaperone DnaK | ||||||
![]() | CHAPERONE / ATPase | ||||||
Function / homology | ![]() endoplasmic reticulum chaperone complex / endoplasmic reticulum unfolded protein response / ATP-dependent protein folding chaperone / endoplasmic reticulum lumen / ATP binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mrozek, A. / Park, H.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues. Authors: Mrozek, A. / Antoshchenko, T. / Chen, Y. / Zepeda-Velazquez, C. / Smil, D. / Kumar, N. / Lu, H. / Park, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.6 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.1 KB | Display | ![]() |
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Full document | ![]() | 805.5 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d1pC ![]() 8d1qC ![]() 8d1sC ![]() 8d1yC ![]() 8d20C ![]() 8d22C ![]() 5umbS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 44360.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum / Strain: isolate Palo Alto / Uganda / Gene: PFUGPA_02944 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-3FD / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.7 M (NH4)2SO4, 1.2 M Li2SO4, 0.1 M NaCitrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 62702 / % possible obs: 100 % / Redundancy: 19 % / Rrim(I) all: 0.06 / Rsym value: 0.06 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.75→1.86 Å / Num. unique obs: 9890 / Rrim(I) all: 0.53 / Rsym value: 0.51 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UMB Resolution: 1.75→48.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.954 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 25.202 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→48.81 Å
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Refine LS restraints |
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