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 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 C2 H5 N O2 75.067 y GLYCINE peptide linking C9 H17 N4 O5 1 261.255 n 2-(2-CARBOXY-ACETYLAMINO)-5-GUANIDINO-PENTANOIC ACID D-ARGININE WITH 3-OXO-PROPIONIC ACID MODIFICATION L-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/pdb1cvq/pdb pdb_00001cvq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 933.026 HISTONE H3 C-TERMINAL DOMAIN 130-135 1 syn polymer no yes (MGG)(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 1999-09-02 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 _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1CS9 is the parent peptide of the original sequence of IRGERA. 1CT6 is the parent peptide, an analogue peptide of the IRGERA sequence. (In this peptide, ALA was replaced by GLY). RCSB Y RCSB 1999-08-24 REL 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. sample THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5 MM OF PEPTIDE AND 0.1 MM MAB). structures with the lowest energy 50 7 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) 7 lowest energy 5 mM peptide, 0.1 mM mAb; 100 mM phosphate buffer containing 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 DAR 2 n 1 MGG 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 MGG 2 A MGG 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 3.75 0.50 120.30 124.05 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 2 3.95 0.50 120.30 124.25 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 3 3.85 0.50 120.30 124.15 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 4 3.88 0.50 120.30 124.18 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 5 3.79 0.50 120.30 124.09 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 6 3.88 0.50 120.30 124.18 A A A NE CZ NH1 DAR DAR DAR 5 5 5 N 7 3.75 0.50 120.30 124.05 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 1 A DIL 6 71.06 72.99 5 A DIL 6 91.15 76.22 6 A DIL 6 91.31 78.58 7 A DIL 6 102.80 -65.70 SOLUTION STRUCTURE OF THE ANALOGUE RETRO-INVERSO MGREGRIGGC IN CONTACT WITH THE MONOCLONAL ANTIBODY MAB 4X11, NMR, 7 STRUCTURES 1 N N covale 1.358 both A MGG 2 A C MGG 1 1_555 A DGL 3 A N DGL 2 1_555 covale 1.346 both A DGL 3 A C DGL 2 1_555 A GLY 4 A N GLY 3 1_555 covale 1.350 both A GLY 4 A C GLY 3 1_555 A DAR 5 A N DAR 4 1_555 covale 1.348 both A DAR 5 A C DAR 4 1_555 A DIL 6 A N DIL 5 1_555 covale 1.342 both A DIL 6 A C DIL 5 1_555 A GLY 7 A N GLY 6 1_555 covale 1.330 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 1CVQ PDB 1 1CVQ 2 10 1CVQ 2 10 1CVQ A 1 1 9 BINDING SITE FOR RESIDUE NH2 A 10 A NH2 10 Software 1 A CYS 9 A CYS 8 1 1_555 1 P 1