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Yorodumi- PDB-1cwz: Solution structure of the analogue retro-inverso (MA-S)REGRIGGC i... -
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-Basic information
Entry | Database: PDB / ID: 1cwz | ||||||
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Title | Solution structure of the analogue retro-inverso (MA-S)REGRIGGC 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 | ||||||
Function / homology | METHYLMALONIC ACID Function and homology information | ||||||
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 | 1cwz.cif.gz | 22.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cwz.ent.gz | 16.4 KB | Display | PDB format |
PDBx/mmJSON format | 1cwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cwz_validation.pdf.gz | 364 KB | Display | wwPDB validaton report |
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Full document | 1cwz_full_validation.pdf.gz | 389.2 KB | Display | |
Data in XML | 1cwz_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 1cwz_validation.cif.gz | 3.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cwz ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cwz | 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: 846.980 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN: Residues 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 RESIDUE PRESENT A D-CONFIGURATION EXCEPT CYS. TWO RI(MA) DIASTEREISOMERS WERE OBTAINED AND COULDN'T BE SEPARATED. |
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#2: Chemical | ChemComp-DXX / |
-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 OF MAB) |
-Sample preparation
Details | Contents: 5MM PEPTIDE, 0.1 MM MAB. 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE |
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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 |