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Open data
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Basic information
| Entry | Database: PDB / ID: 1zag | |||||||||
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| Title | HUMAN ZINC-ALPHA-2-GLYCOPROTEIN | |||||||||
Components | PROTEIN (ZINC-ALPHA-2-GLYCOPROTEIN) | |||||||||
Keywords | LIPID MOBILIZATION FACTOR / SECRETED MHC CLASS I HOMOLOG | |||||||||
| Function / homology | Function and homology informationMiscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.8 Å | |||||||||
Authors | Chirino, A.J. / Sanchez, L.M. / Bjorkman, P.J. | |||||||||
Citation | Journal: Science / Year: 1999Title: Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules. Authors: Sanchez, L.M. / Chirino, A.J. / Bjorkman, P. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Biochemical characterization and crystalization of human Zn-alpha2-glycoprotein, a soluble class I major histocompatibility complex homolog. Authors: Sanchez, L.M. / Lopez-Otin, C. / Bjorkman, P.J. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988 Title: Complete amino acid sequence of human plasma Zn-alpha 2-glycoprotein and its homology to histocompatibility antigens. Authors: Araki, T. / Gejyo, F. / Takagaki, K. / Haupt, H. / Schwick, H.G. / Burgi, W. / Marti, T. / Schaller, J. / Rickli, E. / Brossmer, R. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 1zag.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb1zag.ent.gz | 194.3 KB | Display | PDB format |
| PDBx/mmJSON format | 1zag.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 1zag_validation.pdf.gz | 735.4 KB | Display | wwPDB validaton report |
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| Full document | 1zag_full_validation.pdf.gz | 771.6 KB | Display | |
| Data in XML | 1zag_validation.xml.gz | 28.5 KB | Display | |
| Data in CIF | 1zag_validation.cif.gz | 41.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1zag ftp://data.pdbj.org/pub/pdb/validation_reports/za/1zag | HTTPS FTP |
-Related structure data
| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| 4 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
-Protein / Non-polymers , 2 types, 8 molecules ABCD

| #1: Protein | Mass: 31684.404 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P25311#7: Water | ChemComp-HOH / | |
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-Sugars , 5 types, 12 molecules 
| #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG Source method: isolated from a genetically manipulated source |
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| #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG Source method: isolated from a genetically manipulated source |
| #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG Source method: isolated from a genetically manipulated source |
| #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / ZN-ALPHA-2-GLYCOPROTEIN / ZAG Source method: isolated from a genetically manipulated source |
| #6: Sugar | ChemComp-NAG / |
-Details
| Has protein modification | Y |
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| Nonpolymer details | NO ATTEMPT HAS BEEN MADE TO MODEL OR OTHERWISE TAKE THE UNKNOWN LIGAND'S DENSITY INTO ACCOUNT ...NO ATTEMPT HAS BEEN MADE TO MODEL OR OTHERWISE TAKE THE UNKNOWN LIGAND'S DENSITY INTO ACCOUNT DURING REFINEMENT |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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| Crystal grow | pH: 5 Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD WITH 30% POLYETHYLENE GLYCOL 2000 MONOMETHYLETHER, 0.2M AMMONIUM ACETATE, AND 0.1M SODIUM ACETATE BUFFER (PH 5.0) | ||||||||||||||||||||||||||||||||||||||||||
| Crystal grow | *PLUS pH: 7 / Method: vapor diffusionDetails: Sanchez, L.M., (1997) Proc.Nat.Acad.Sci.USA, 94, 4626. | ||||||||||||||||||||||||||||||||||||||||||
| Components of the solutions | *PLUS
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
| Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: YALE MIRRORS |
| Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 2.8→100 Å / Num. obs: 39365 / % possible obs: 95.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 27 |
| Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.5 / % possible all: 75.7 |
| Reflection shell | *PLUS % possible obs: 75.7 % |
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Processing
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| Refinement | Method to determine structure: MIRAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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| Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.15 Å2 / ksol: 0.26 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 54.3 Å2
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| Refine analyze |
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| Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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| Refine LS restraints |
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| Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 300
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| LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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| Xplor file |
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| Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints | *PLUS
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Homo sapiens (human)
X-RAY DIFFRACTION
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