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Yorodumi- PDB-1ieh: SOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ieh | ||||||
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Title | SOLUTION STRUCTURE OF A SOLUBLE SINGLE-DOMAIN ANTIBODY WITH HYDROPHOBIC RESIDUES TYPICAL OF A VL/VH INTERFACE | ||||||
Components | BRUC.D4.4 | ||||||
Keywords | IMMUNE SYSTEM / two pleated beta-sheet / immunoglobulin beta-barrel | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | SOLUTION NMR / simulated annealing using torsion angle, cartesian dynamics | ||||||
Authors | Vranken, W. / Tolkatchev, D. / Xu, P. / Tanha, J. / Chen, Z. / Narang, S. / Ni, F. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface. Authors: Vranken, W. / Tolkatchev, D. / Xu, P. / Tanha, J. / Chen, Z. / Narang, S. / Ni, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ieh.cif.gz | 390.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ieh.ent.gz | 336.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ieh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ieh_validation.pdf.gz | 343.6 KB | Display | wwPDB validaton report |
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Full document | 1ieh_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 1ieh_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 1ieh_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1ieh ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1ieh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 14618.006 Da / Num. of mol.: 1 / Fragment: SINGLE DOMAIN ANTIBODY FROM A NAIVE LLAMA LIBRARY Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D combined 13C/15N-separated NOESY |
-Sample preparation
Details | Contents: 10mM sodium phosphate 150mM NaCl 0.2mM EDTA / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0.16 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing using torsion angle, cartesian dynamics Software ordinal: 1 Details: NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS ...Details: NO MANUAL ASSIGNMENTS OF NOE PEAKS WERE INITIALLY PERFORMED - THE GLOBAL FOLD OF THE PROTEIN WAS DETERMINED USING RESTRAINTS WITH LOW AMBIGUITY. THE SET OF GLOBAL FOLD STRUCTURES SERVED AS AN ASSIGNMENT FILTER TO REDUCE THE AMBIGUITY OF THE OTHER RESTRAINTS. THE RESTRAINT LIST AND STRUCTURES WERE FURTHER REFINED BY MANUALLY CHOOSING POSSIBILITIES FROM THE RESTRAINTS WITH LOW AMBIGUITY (BASED ON THE SPECTRA). | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 150 / Conformers submitted total number: 10 |