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Yorodumi- PDB-8egi: X-ray structure of carbonmonoxy hemoglobin in complex with VZHE039-NO -
+Open data
-Basic information
Entry | Database: PDB / ID: 8egi | ||||||||||||
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Title | X-ray structure of carbonmonoxy hemoglobin in complex with VZHE039-NO | ||||||||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||||||||
Keywords | OXYGEN TRANSPORT / Hemoglobin / sickle cell disease / antisickling / nitric oxide / oxygen equilibrium curve | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Donkor, A.K. / Musayev, F.N. / Safo, M.K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Molecules / Year: 2022 Title: Design, Synthesis, and Investigation of Novel Nitric Oxide (NO)-Releasing Aromatic Aldehydes as Drug Candidates for the Treatment of Sickle Cell Disease. Authors: Huang, B. / Ghatge, M.S. / Donkor, A.K. / Musayev, F.N. / Deshpande, T.M. / Al-Awadh, M. / Alhashimi, R.T. / Zhu, H. / Omar, A.M. / Telen, M.J. / Zhang, Y. / McMahon, T.J. / Abdulmalik, O. / Safo, M.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8egi.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8egi.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 8egi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8egi_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 8egi_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 8egi_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 8egi_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/8egi ftp://data.pdbj.org/pub/pdb/validation_reports/eg/8egi | HTTPS FTP |
-Related structure data
Related structure data | 3ic0S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 15281.550 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: 16021.396 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 , 4 types, 454 molecules
#3: Chemical | ChemComp-CMO / #4: Chemical | ChemComp-HEM / #5: Chemical | #6: 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: 2.1 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 mg/dL of CO-ligated Hb crystallized using 10-20% PEG 6000, 100 mM Hepes, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 22, 2021 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→28.86 Å / Num. obs: 25048 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 23.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.039 / Rrim(I) all: 0.113 / Net I/σ(I): 15.7 / Num. measured all: 202614 / Scaling rejects: 92 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IC0 Resolution: 2.3→28.858 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.1 Å2 / Biso mean: 25.9502 Å2 / Biso min: 9.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→28.858 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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