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Yorodumi- PDB-2dcv: The solution structure of horseshoe crab antimicrobial peptide ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dcv | ||||||
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Title | The solution structure of horseshoe crab antimicrobial peptide tachystatin b with the inhibitory cystine-knot motif | ||||||
Components | Tachystatin-B1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial / cystine-knot | ||||||
Function / homology | Function and homology information defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Tachypleus tridentatus (Chinese horseshoe crab) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Fujitani, N. / Kohno, T. | ||||||
Citation | Journal: J.Pept.Sci. / Year: 2007 Title: The solution structure of horseshoe crab antimicrobial peptide tachystatin B with an inhibitory cystine-knot motif Authors: Fujitani, N. / Kouno, T. / Nakahara, T. / Takaya, K. / Osaki, T. / Kawabata, S. / Mizuguchi, M. / Aizawa, T. / Demura, M. / Nishimura, S. / Kawano, K. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Horseshoe crab hemocyte-derived antimicrobial polypeptides, tachystatins, with sequence similarity to spider neurotoxins Authors: Osaki, T. / Omotezako, M. / Nagayama, R. / Hirata, M. / Iwanaga, S. / Kasahara, J. / Hattori, J. / Ito, I. / Sugiyama, H. / Kawabata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dcv.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dcv.ent.gz | 223.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dcv_validation.pdf.gz | 337.6 KB | Display | wwPDB validaton report |
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Full document | 2dcv_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 2dcv_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2dcv_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/2dcv ftp://data.pdbj.org/pub/pdb/validation_reports/dc/2dcv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4926.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tachypleus tridentatus (Chinese horseshoe crab) Cell: hemocyte / References: UniProt: P0C1Z8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | pH: 3.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |