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- PDB-1cs9: SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL AN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cs9 | ||||||
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Title | SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES | ||||||
![]() | HISTONE H3 PEPTIDE | ||||||
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Function / homology | ![]() chromatin organization => GO:0006325 / DNA replication-dependent chromatin assembly / nuclear chromosome / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Method | ![]() | ||||||
![]() | Phan Chan Du, A. / Petit, M.C. / Guichard, G. / Briand, J.P. / Muller, S. / Cung, M.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.7 KB | Display | ![]() |
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PDB format | ![]() | 14.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 920.050 Da / Num. of mol.: 1 / Fragment: C-TERMINAL REGION 130-135 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THE C-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB 4X11 MONOCLONAL ANTIBODY (IGG1). ...Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THE C-TERMINAL REGION 130-135 OF HISTONE H3 BOUND TO THE MAB 4X11 MONOCLONAL ANTIBODY (IGG1). THE SEQUENCE CGG WAS ADDED TO THE N- TERMINUS OF THE IRGERA SEQUENCE AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS VIA THE CYS THIOL GROUP. References: UniProt: P16106, UniProt: P68431*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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NMR experiment | Type![]() ![]() ![]() |
NMR details | Text: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM OF PEPTIDE AND 0.1MM OF MAB) |
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Sample preparation
Details | Contents: 5 MM PEPTIDE, 0.1MM 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![]() |
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Processing
NMR software |
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Refinement | Method: ENERGY MINIMIZATION MOLECULAR DYNAMICS / Software ordinal: 1 Details: ENERGY MINIMISATION. A DISTANT 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 ...Details: ENERGY MINIMISATION. A DISTANT 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. IN THE PDB, NH3+ IS INCLUDED IN THE RESIDUE CYS, AND COO- IS INCLUDED IN THE RESIDUE ALA. THE RESIDUE GLU HAS MISSING ATOMS HE2 IN ALL STRUCTURES BECAUSE IN DISCOVER, THIS RESIDUE IS MODELLED AS A CHARGED GROUP(WE HAVE COO- AND NOT COOH). | ||||||||||||||||
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 |