[English] 日本語
![](img/lk-miru.gif)
- PDB-1qxd: Structural Basis for the Potent Antisickling Effect of a Novel Cl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qxd | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Basis for the Potent Antisickling Effect of a Novel Class of 5-Membered Heterocyclic Aldehydic Compounds | ||||||
![]() |
| ||||||
![]() | OXYGEN STORAGE/TRANSPORT / allosteric / antisickling / relaxed state / hemoglobin / sickle cell / furfural / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Safo, M.K. / Abdulmalik, O. / Danso-Danquah, R. / Nokuri, S. / Joshi, G.S. / Musayev, F.N. / Asakura, T. / Abraham, D.J. | ||||||
![]() | ![]() Title: Structural basis for the potent antisickling effect of a novel class of five-membered heterocyclic aldehydic compounds Authors: Safo, M.K. / Abdulmalik, O. / Danso-Danquah, R. / Burnett, J.C. / Nokuri, S. / Joshi, G.S. / Musayev, F.N. / Asakura, T. / Abraham, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 131.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qxeC ![]() 1bbbS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: alpha chain / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Fragment: beta chain / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 4 types, 314 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FU2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FU2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-HEM / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.3 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.5 Details: ammonium phosphate and sulfate, pH 6.5, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Method: other | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 13, 2002 / Details: mirrors |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→70 Å / Num. all: 32647 / Num. obs: 32647 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1991 / % possible all: 94.1 |
Reflection | *PLUS Lowest resolution: 69.14 Å / % possible obs: 97 % / Num. measured all: 124853 |
Reflection shell | *PLUS % possible obs: 94.1 % / Num. unique obs: 1991 / Num. measured obs: 9905 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1BBB Resolution: 2.25→69.14 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.708 Å2 / ksol: 0.384124 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
| |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.6 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→69.14 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.37 Å |