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, 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 S 121.158 y CYSTEINE L-peptide linking C6 H15 N4 O2 1 175.209 D-ARGININE D-peptide linking C5 H9 N O4 147.129 D-GLUTAMIC ACID D-peptide linking C6 H13 N O2 131.173 D-ISOLEUCINE D-peptide linking C4 H6 O4 118.088 METHYLMALONIC ACID non-polymer C2 H5 N O2 75.067 y GLYCINE peptide linking H2 N 16.023 AMINO GROUP non-polymer 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/pdb1cw8/pdb pdb_00001cw8 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 846.980 HISTONE H3 C-TERMINAL DOMAIN 130-135 1 syn polymer 118.088 METHYLMALONIC ACID 1 syn non-polymer no yes (DAR)(DGL)G(DAR)(DIL)GGC(NH2) REGRIGGCX A polypeptide(L) n n n n n n n n n database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1999-09-03 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 _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1CS9 is the parent peptide. 1CT6 is a parent analogue peptide of the IRGERA sequence. (in this peptide, ALA was replaced by GLY). 1 CVQ is the retro-inverso analogue of 1CT6. RCSB Y RCSB 1999-08-26 REL DXX METHYLMALONIC ACID 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. Two RI(mA) diastereisomers were obtained and couldn't be separated. sample The peptide/mAb molar ratio was adjusted to 50/1(i.e. 5 mM of peptide and 0.1 mM of mAb) structures with the lowest energy 50 6 COSY, TOCSY, NOESY 0.1M phosphate 7 1 atm 277 K 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. Energy minimisation Molecular dynamics (Simulated Annealing) 5 lowest energy 5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containning 0.02% sodium azide 95% H2O/5% D2O Guntert, Wuthrich structure solution DYANA 1.4 Molecular Simulations Inc., San Diego, CA structure solution Discover 3 Molecular Simulations Inc., San Diego, CA refinement Discover 3 Bruker collection XwinNMR 1.2 400 Bruker DRX DXX 1 2 DXX DXX 1 A DAR 2 n 1 DAR 2 A DGL 3 n 2 DGL 3 A GLY 4 n 3 GLY 4 A DAR 5 n 4 DAR 5 A DIL 6 n 5 DIL 6 A GLY 7 n 6 GLY 7 A GLY 8 n 7 GLY 8 A CYS 9 n 8 CYS 9 A NH2 10 n 9 NH2 10 A author_defined_assembly 1 monomeric A DAR 2 D-ARGININE A DAR 1 ARG A DGL 3 D-GLUTAMIC ACID A DGL 2 GLU A DAR 5 D-ARGININE A DAR 4 ARG A DIL 6 D-ISOLEUCINE A DIL 5 ILE 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 3.85 0.50 120.30 124.15 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 1 3.64 0.50 120.30 123.94 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 2 3.72 0.50 120.30 124.02 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 2 3.80 0.50 120.30 124.10 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 3 3.72 0.50 120.30 124.02 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 3 3.73 0.50 120.30 124.03 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 4 3.69 0.50 120.30 123.99 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 4 3.64 0.50 120.30 123.94 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 5 3.61 0.50 120.30 123.91 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 5 3.65 0.50 120.30 123.95 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 6 3.67 0.50 120.30 123.97 A A A NE CZ NH2 DAR DAR DAR 2 2 2 N 6 3.84 0.50 120.30 124.14 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 2 A DIL 6 115.96 -69.49 3 A DIL 6 153.26 -70.71 5 A DIL 6 85.06 73.07 6 A DIL 6 110.22 -66.85 SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO (mA-R)REGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 6 STRUCTURES 1 N N 2 N N covale 1.346 both A DXX 1 B C DXX 1_555 A DAR 2 A N DAR 1 1_555 covale 1.357 both A DAR 2 A C DAR 1 1_555 A DGL 3 A N DGL 2 1_555 covale 1.345 both A DGL 3 A C DGL 2 1_555 A GLY 4 A N GLY 3 1_555 covale 1.354 both A GLY 4 A C GLY 3 1_555 A DAR 5 A N DAR 4 1_555 covale 1.347 both A DAR 5 A C DAR 4 1_555 A DIL 6 A N DIL 5 1_555 covale 1.346 both A DIL 6 A C DIL 5 1_555 A GLY 7 A N GLY 6 1_555 covale 1.327 both A CYS 9 A C CYS 8 1_555 A NH2 10 A N NH2 9 1_555 DNA BINDING PROTEIN PSEUDOMIMETIC, SYNTHETIC PEPTIDE, RETRO-INVERSO ANALOGUE, TR-NOE, ANTIGEN- ANTIBODY COMPLEX, DNA BINDING PROTEIN 1CW8 PDB 1 1CW8 2 10 1CW8 2 10 1CW8 A 1 1 9 BINDING SITE FOR RESIDUE DXX A 1 A DXX 1 Software 2 A DAR 2 A DAR 1 2 1_555 A DGL 3 A DGL 2 2 1_555 1 P 1