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Open data
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Basic information
Entry | Database: PDB / ID: 7jy3 | ||||||
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Title | Structure of HbA with compound 23 (PF-07059013) | ||||||
![]() | (Hemoglobin subunit ...) x 2 | ||||||
![]() | OXYGEN TRANSPORT / hemoglobin | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jasti, J. | ||||||
![]() | ![]() Title: PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease. Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, ...Authors: Gopalsamy, A. / Aulabaugh, A.E. / Barakat, A. / Beaumont, K.C. / Cabral, S. / Canterbury, D.P. / Casimiro-Garcia, A. / Chang, J.S. / Chen, M.Z. / Choi, C. / Dow, R.L. / Fadeyi, O.O. / Feng, X. / France, S.P. / Howard, R.M. / Janz, J.M. / Jasti, J. / Jasuja, R. / Jones, L.H. / King-Ahmad, A. / Knee, K.M. / Kohrt, J.T. / Limberakis, C. / Liras, S. / Martinez, C.A. / McClure, K.F. / Narayanan, A. / Narula, J. / Novak, J.J. / O'Connell, T.N. / Parikh, M.D. / Piotrowski, D.W. / Plotnikova, O. / Robinson, R.P. / Sahasrabudhe, P.V. / Sharma, R. / Thuma, B.A. / Vasa, D. / Wei, L. / Wenzel, A.Z. / Withka, J.M. / Xiao, J. / Yayla, H.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.6 KB | Display | ![]() |
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PDB format | ![]() | 206 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jxzC ![]() 7jy0C ![]() 7jy1C ![]() 3whmS S: Starting model for refinement 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
-Hemoglobin subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 407 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/O4B.gif)
![](data/chem/img/VUD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/O4B.gif)
![](data/chem/img/VUD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-OXY / #5: Chemical | ChemComp-O4B / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M lithium sulfate, 30-32% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→44.68 Å / Num. obs: 55793 / % possible obs: 96.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Net I/av σ(I): 11.3 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.48→1.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 496 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3WHM Resolution: 1.48→29.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.111
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Displacement parameters | Biso max: 106.1 Å2 / Biso mean: 26.28 Å2 / Biso min: 8.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.49 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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