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Open data
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Basic information
Entry | Database: PDB / ID: 2w6v | ||||||
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Title | Structure of Human deoxy Hemoglobin A in complex with Xenon | ||||||
![]() | (HEMOGLOBIN SUBUNIT ...) x 2 | ||||||
![]() | OXYGEN TRANSPORT / PACKING DEFECTS / HYDROPHOBIC CAVITIES | ||||||
Function / homology | ![]() 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 / platelet aggregation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miele, A.E. / Draghi, F. / Sciara, G. / Johnson, K.A. / Renzi, F. / Vallone, B. / Brunori, M. / Savino, C. | ||||||
![]() | ![]() Title: Pattern of Cavities in Globins: The Case of Human Hemoglobin. Authors: Savino, C. / Miele, A.E. / Draghi, F. / Johnson, K.A. / Sciara, G. / Brunori, M. / Vallone, B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.8 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2w6wC ![]() 2w72C ![]() 4hhbS 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 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Fragment: CHAIN BETA, RESIDUES 2-147 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 601 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-XE / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.19 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 3.2M (NH4)2SO4, 0.1M (NH4)H2PO4, 0.3M (NH4)2HPO4, PH 6.5, 0.2% DITHIONITE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61 Å / Num. obs: 49841 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.85 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.79→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4HHB Resolution: 1.8→22.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.007 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY AND THEIR OCCUPANCY PUT TO 0.0
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→22.9 Å
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