+Open data
-Basic information
Entry | Database: PDB / ID: 2m2y | ||||||
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Title | Solution structure of the antimicrobial peptide Btd-2[3,4] | ||||||
Components | BTD-2[3,4] | ||||||
Keywords | ANTIMICROBIAL PROTEIN / theta-defensin / cyclic peptides / cyclic cystine ladder / disulfide bond / antimicrobial peptide | ||||||
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 | 2m2y.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m2y.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2m2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/2m2y ftp://data.pdbj.org/pub/pdb/validation_reports/m2/2m2y | HTTPS FTP |
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-Related structure data
Related structure data | 2m1pC 2m2gC 2m2hC 2m2sC 2m2xC C: citing same article (ref.) |
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Similar structure data | |
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: Protein/peptide | Mass: 2090.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Acyclic analogue of the theta-defensin BTD-2. Disulfide bonds join residues 2-11, 4-9, and 13-18. | ||||||||||||||||||||||||
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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: 96 / NOE intraresidue total count: 57 / NOE long range total count: 3 / NOE medium range total count: 3 / NOE sequential total count: 33 / Hydrogen bond constraints total count: 10 / Protein chi angle constraints total count: 5 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 14 / Protein psi angle constraints total count: 10 | ||||||||||||||||||||||||||||||||||||
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 |