1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Phan Chan Du, A. Petit, M.C. Guichard, G. Briand, J.P. Muller, S. Cung, M.T. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 40 5720 5727 10.1021/bi001151h 11341837 Structure of antibody-bound peptides and retro-inverso analogues. A transferred nuclear Overhauser effect spectroscopy and molecular dynamics approach. 2001 10.2210/pdb1cs9/pdb pdb_00001cs9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 920.050 HISTONE H3 PEPTIDE C-TERMINAL REGION 130-135 1 syn polymer no no CGGIRGERA CGGIRGERA A polypeptide(L) n n n n n n n n n database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1999-09-02 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 1999-08-18 REL 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. sample THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM OF PEPTIDE AND 0.1MM OF MAB) structures with the lowest energy 50 7 TOCSY, NOESY, COSY 0.1M PHOSPHATE 7 1 atm 277 K 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). ENERGY MINIMIZATION MOLECULAR DYNAMICS 7 lowest energy 5 MM PEPTIDE, 0.1MM MAB; 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE GUNTERT, WUTHRICH structure solution DYANA 1.4 MOLECULAR SIMULATIONS INC., SAN DIEGO, CA structure solution Discover 3 MOLECULAR SIMULATIONS INC. refinement Discover 3 400 Bruker DRX CYS 1 n 1 CYS 1 A GLY 2 n 2 GLY 2 A GLY 3 n 3 GLY 3 A ILE 4 n 4 ILE 4 A ARG 5 n 5 ARG 5 A GLY 6 n 6 GLY 6 A GLU 7 n 7 GLU 7 A ARG 8 n 8 ARG 8 A ALA 9 n 9 ALA 9 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 3.72 0.50 120.30 124.02 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 1 3.69 0.50 120.30 123.99 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 2 3.83 0.50 120.30 124.13 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 2 3.78 0.50 120.30 124.08 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 3 3.76 0.50 120.30 124.06 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 3 3.72 0.50 120.30 124.02 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 4 3.88 0.50 120.30 124.18 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 4 3.77 0.50 120.30 124.07 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 5 3.80 0.50 120.30 124.10 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 5 3.83 0.50 120.30 124.13 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 6 3.74 0.50 120.30 124.04 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 6 3.69 0.50 120.30 123.99 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 7 3.74 0.50 120.30 124.04 A A A NE CZ NH1 ARG ARG ARG 5 5 5 N 7 3.53 0.50 120.30 123.83 A A A NE CZ NH1 ARG ARG ARG 8 8 8 N 2 A ARG 5 -154.01 -97.81 3 A GLU 7 -158.65 -96.90 3 A ARG 8 -160.87 65.11 4 A ARG 5 -158.30 85.41 4 A GLU 7 -163.13 119.21 4 A ARG 8 -156.61 89.73 5 A ARG 5 -157.65 -81.59 5 A GLU 7 -157.47 -84.79 5 A ARG 8 -157.62 -66.04 6 A GLU 7 -155.53 83.01 7 A GLU 7 -160.49 111.28 7 A ARG 8 -151.36 85.82 SOLUTION STRUCTURE OF CGGIRGERA IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES 1 N N DNA BINDING PROTEIN SYNTHETIC PEPTIDE, TR-NOE, ANTIGEN-ANTIBODY COMPLEX, DNA BINDING PROTEIN H31_HUMAN UNP 1 P16106 130 135 1CS9 4 9 P16106 A 1 4 9 1 P 1