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Yorodumi- PDB-1cvq: SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC IN CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cvq | ||||||
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Title | SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES | ||||||
Components | HISTONE H3 | ||||||
Keywords | DNA BINDING PROTEIN / PSEUDOMIMETIC / SYNTHETIC PEPTIDE / RETRO-INVERSO ANALOGUE / TR-NOE / ANTIGEN- ANTIBODY COMPLEX | ||||||
Method | SOLUTION NMR / Energy minimisation Molecular dynamics (simulated Annealing) | ||||||
Authors | Phan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach. Authors: Phan-Chan-Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cvq.cif.gz | 21.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cvq.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cvq_validation.pdf.gz | 349.7 KB | Display | wwPDB validaton report |
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Full document | 1cvq_full_validation.pdf.gz | 371.2 KB | Display | |
Data in XML | 1cvq_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 1cvq_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/1cvq ftp://data.pdbj.org/pub/pdb/validation_reports/cv/1cvq | 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: 933.026 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN 130-135 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence CGG was added as a linker to the dextran matrix in Biacore experiments via the Cys thiol group. NH2-CO was added at the C-terminal ...Details: The peptide was chemically synthesized. The sequence CGG was added as a linker to the dextran matrix in Biacore experiments via the Cys thiol group. NH2-CO was added at the C-terminal extremity of the retro-inverso peptide in order to mimic the N-terminal of the parent peptide. All non Glycine residues present a D-configuration except CYS. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: COSY, TOCSY, NOESY |
NMR details | Text: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5 MM OF PEPTIDE AND 0.1 MM MAB). |
-Sample preparation
Details | Contents: 5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containing 0.02% sodium azide Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 0.1M phosphate / pH: 7 / Pressure: 1 atm / Temperature: 277 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 400 MHz |
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-Processing
NMR software |
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Refinement | Method: Energy minimisation Molecular dynamics (simulated Annealing) Software ordinal: 1 Details: The structures are based on a set of 35 to 60 backbone-backbone, backbone-side chain and side chain-side chain distance restraints. The phi angle for the non glycine D-residues was ...Details: The structures are based on a set of 35 to 60 backbone-backbone, backbone-side chain and side chain-side chain distance restraints. The phi angle for the non glycine D-residues was constrained between 0 and 175. A distance dependent dielectric constant equal to 4r was applied. The net electric charges were decreased, while those of the N and C terminal charged groups were neglected. | ||||||||||||||||||||
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: 7 |