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Yorodumi- PDB-1nih: Structure of deoxy-quaternary haemoglobin with liganded beta subunits -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nih | ||||||
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Title | Structure of deoxy-quaternary haemoglobin with liganded beta subunits | ||||||
Components |
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Keywords | OXYGEN TRANSPORT | ||||||
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 / regulation of blood pressure / 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 / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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 / Resolution: 2.6 Å | ||||||
Authors | Luisi, B. / Liddington, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Structure of deoxy-quaternary haemoglobin with liganded beta subunits. Authors: Luisi, B. / Liddington, B. / Fermi, G. / Shibayama, N. #1: Journal: Acc.Chem.Res. / Year: 1987 Title: Stereochemistry of Cooperative Mechanisms in Hemoglobin Authors: Perutz, M.F. / Fermi, G. / Luisi, B. / Shaanan, B. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nih.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nih.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nih_validation.pdf.gz | 806.3 KB | Display | wwPDB validaton report |
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Full document | 1nih_full_validation.pdf.gz | 847.2 KB | Display | |
Data in XML | 1nih_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1nih_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1nih ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1nih | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 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) / 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) / References: UniProt: P68871 |
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-Non-polymers , 5 types, 59 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-IHP / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: unknown / Details: crystals were grown under a CO atomosphere. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 17218 / Num. measured all: 34793 / Rmerge(I) obs: 0.058 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.214 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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Software | *PLUS Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |