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Yorodumi- PDB-2mmt: Lasso peptide-based integrin inhibitor: Microcin J25 variant with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mmt | ||||||
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Title | Lasso peptide-based integrin inhibitor: Microcin J25 variant with RGDF substitution of Gly12-Ile13-Gly14-Thr15 | ||||||
Components | Microcin J25 RGDF mutant | ||||||
Keywords | ANTIBIOTIC / lasso peptide / epitope grafting / integrin inhibitor / drug design / molecular scaffolds / molecular dynamics | ||||||
Function / homology | killing of cells of another organism / defense response to bacterium / extracellular region / Microcin J25 Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Hegemann, J.D. / Zimmermann, M. / Knappe, T.A. / Xie, X. / Marahiel, M.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Rational improvement of the affinity and selectivity of integrin binding of grafted lasso peptides. Authors: Hegemann, J.D. / De Simone, M. / Zimmermann, M. / Knappe, T.A. / Xie, X. / Di Leva, F.S. / Marinelli, L. / Novellino, E. / Zahler, S. / Kessler, H. / Marahiel, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mmt.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mmt.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/2mmt ftp://data.pdbj.org/pub/pdb/validation_reports/mm/2mmt | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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 | Mass: 2274.490 Da / Num. of mol.: 1 / Fragment: UNP residues 38-58 / Mutation: G12R/I13G/G14D/T15F / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q9X2V7 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 12.6 mM MCCJ25(RGDF), methanol / Solvent system: methanol |
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Sample | Conc.: 12.6 mM / Component: MCCJ25(RGDF)-1 |
Sample conditions | Pressure: 1.0 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: BRUKER AVANCE / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software | Name: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler / Classification: refinement |
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Refinement | Method: 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: 50 / Conformers submitted total number: 15 |