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Yorodumi- PDB-2m2h: Solution structure of the antimicrobial peptide [Aba3,7,12,16]BTD-2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m2h | ||||||
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Title | Solution structure of the antimicrobial peptide [Aba3,7,12,16]BTD-2 | ||||||
Components | [Aba3,7,12,16]BTD-2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / theta-defensin / cyclic peptides / cyclic cystine ladder / disulfide bond / antimicrobial peptide | ||||||
Function / homology | [Aba3,7,12,16]BTD-2 Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Conibear, A.C. / Rosengren, K. / Daly, N.L. / Troiera Henriques, S. / Craik, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The cyclic cystine ladder in theta-defensins is important for structure and stability, but not antibacterial activity. Authors: Conibear, A.C. / Rosengren, K.J. / Daly, N.L. / Henriques, S.T. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m2h.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m2h.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2m2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m2h_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 2m2h_full_validation.pdf.gz | 522.4 KB | Display | |
Data in XML | 2m2h_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 2m2h_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/2m2h ftp://data.pdbj.org/pub/pdb/validation_reports/m2/2m2h | HTTPS FTP |
-Related structure data
Related structure data | 2m1pC 2m2gC 2m2sC 2m2xC 2m2yC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | [ |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Head-to-tail (Arg-Gly) cyclic peptide. Residues 3, 7, 12, and 16 are replaced by alpha-aminobutyric acid. | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: Structures were calculated using the scripts from the RECOORD database. Used to calculate preliminary structures | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 110 / NOE intraresidue total count: 52 / NOE long range total count: 8 / NOE medium range total count: 10 / NOE sequential total count: 40 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 4 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 16 / Protein psi angle constraints total count: 14 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |