+Open data
-Basic information
Entry | Database: PDB / ID: 7uf6 | |||||||||
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Title | Crystal structure of liganded Hb with the 5-HMF analog, MMA509 | |||||||||
Components | (Hemoglobin subunit ...) x 2 | |||||||||
Keywords | OXYGEN TRANSPORT / hemoglobin / 5-HMF / sickle cell disease / antisickling / oxygen equilibrium / aromatic aldehydes | |||||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / 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 / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Donkor, A.K. / Musayev, F.N. / Safo, M.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Improving the antisickling activity of furaldehyde Authors: El-Araby, M.E. / Omar, A.M. / Ghatge, M.S. / Musayev, F.N. / Donkor, A.K. / Paredes, S.D. / 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 | 7uf6.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uf6.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 7uf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uf6_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7uf6_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7uf6_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 7uf6_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7uf6 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7uf6 | HTTPS FTP |
-Related structure data
Related structure data | 7uf7C 3ic0S S: Starting model for refinement C: citing same article (ref.) |
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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, 768 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #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: 7.4 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: Dec 2, 2020 / 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→28.3 Å / Num. obs: 38189 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 24.8 / Num. measured all: 284459 / Scaling rejects: 195 | ||||||||||||||||||||||||||||||
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→28.298 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.26 / 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: 69.55 Å2 / Biso mean: 21.6014 Å2 / Biso min: 6.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→28.298 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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