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Open data
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Basic information
Entry | Database: PDB / ID: 2m79 | ||||||
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Title | [Asp2,11]RTD-1 | ||||||
![]() | [Asp2,11]RTD-1 | ||||||
![]() | CELL ADHESION / theta-defensin / cyclic peptides / cyclic cystine ladder / integrin-binding | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Conibear, A.C. / Bochen, A. / Rosengren, K. / Kessler, H. / Craik, D.J. | ||||||
![]() | ![]() Title: The Cyclic Cystine Ladder of Theta-Defensins as a Stable, Bifunctional Scaffold: A Proof-of-Concept Study Using the Integrin-Binding RGD Motif Authors: Conibear, A.C. / Bochen, A. / Rosengren, K.J. / Stupar, P. / Wang, C. / Kessler, H. / Craik, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.9 KB | Display | ![]() |
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Full document | ![]() | 544.8 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | [ Mass: 2094.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase peptide synthesis |
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Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: High resolution NMR solution structure of a theta-defensin analogue containing the RGD integrin-binding sequence. Head-to-tail (Arg-Gly) cyclic peptide. | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | pH: 3 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
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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: 102 / NOE intraresidue total count: 50 / NOE long range total count: 7 / NOE medium range total count: 5 / NOE sequential total count: 40 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 8 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 15 | ||||||||||||||||||||||||||||||||||||
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 / Representative conformer: 1 |