+Open data
-Basic information
Entry | Database: PDB / ID: 7jy0 | ||||||
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Title | Structure of HbA with compound 9 | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / hemoglobin | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin 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 / platelet aggregation / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Jasti, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jy0.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jy0.ent.gz | 210.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jy0_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7jy0_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7jy0_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 7jy0_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/7jy0 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/7jy0 | HTTPS FTP |
-Related structure data
Related structure data | 7jxzC 7jy1C 7jy3C 3whmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871 |
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-Non-polymers , 5 types, 590 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.63→62.75 Å / Num. obs: 67878 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 11.9 / Num. measured all: 214529 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3WHM Resolution: 1.63→62.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.091
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Displacement parameters | Biso max: 116.5 Å2 / Biso mean: 29.32 Å2 / Biso min: 13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→62.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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