[English] 日本語
![](img/lk-miru.gif)
- PDB-8fk6: Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8fk6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed to Human Chemokine CCL7 | ||||||
![]() |
| ||||||
![]() | CYTOKINE / Evasin / Chemokine-binding protein / ticks | ||||||
Function / homology | ![]() negative regulation of chemokine activity / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / chemokine binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol ...negative regulation of chemokine activity / CCR2 chemokine receptor binding / CCR1 chemokine receptor binding / chemokine binding / positive regulation of natural killer cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / C-C chemokine binding / eosinophil chemotaxis / cellular response to ethanol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / cytoskeleton organization / neutrophil chemotaxis / response to gamma radiation / cellular response to type II interferon / intracellular calcium ion homeostasis / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Devkota, S.R. / Bhusal, R.P. / Aryal, P. / Wilce, M.C.J. / Stone, M.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins. Authors: Devkota, S.R. / Aryal, P. / Pokhrel, R. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R.J. / Wilce, M.C.J. / Bhusal, R.P. / Stone, M.J. #1: ![]() Title: Engineering Broad-spectrum Inhibitors of Inflammatory Chemokines from a New Family of Tick Evasins Authors: Devkota, S. / Aryal, P. / Jiao, W. / Perry, A. / Panjikar, S. / Payne, R. / Wilce, M. / Bhusal, R. / Stone, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 85.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 428.6 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7scsC ![]() 7sctC ![]() 7scvC ![]() 8fj0C ![]() 8fj2C ![]() 8fj3C ![]() 8fk8C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11210.546 Da / Num. of mol.: 1 / Mutation: Y44A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 8974.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→49.25 Å / Num. obs: 18937 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 39.4 |
Reflection shell | Resolution: 1.74→1.77 Å / Num. unique obs: 1025 / CC1/2: 0.985 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→40.7 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|