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 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/pdb1cwz/pdb pdb_00001cwz 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: Residues 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 IREGERA SEQUENCE (IN THIS PEPTIDE, ALA WAS REPLACED BY GLY). 1CVQ IS THE RETRO-INVERSO ANALOGUE OF 1CT6. 1CW8 IS THE RETRO-INVERSO ANALOGUE OF 1CS9, MODELLED WITH MR-A. RCSB Y RCSB 1999-08-27 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 RESIDUE 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 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) 6 lowest energy 5MM PEPTIDE, 0.1 MM MAB. 100 MM PHOSPHATE BUFFER CONTAINING 0.02% SODIUM AZIDE GUNTERT, WUTHRICH structure solution DYANA 1.4 MOLECULAR SIMULATIONS INC. structure solution Discover 3 MOLECULAR SIMULATIONS INC. refinement Discover 3 400 Bruker DRX DXS 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 4 A A HG HN2 CYS NH2 9 10 1.14 6 A A O HG GLY CYS 8 9 0.95 6 A A HA3 SG GLY CYS 4 9 1.16 6 A A CA SG GLY CYS 4 9 1.91 6 A A O SG GLY CYS 4 9 2.10 6 A A C SG GLY CYS 4 9 2.15 7 A A CG HG DAR CYS 5 9 0.93 7 A A HA SG DAR CYS 5 9 1.00 7 A A HG2 HG DAR CYS 5 9 1.10 7 A A CB HG DAR CYS 5 9 1.16 7 A A CA SG DAR CYS 5 9 1.65 7 A A CB SG DAR CYS 5 9 1.85 1 3.70 0.50 120.30 124.00 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 1 3.76 0.50 120.30 124.06 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 2 3.63 0.50 120.30 123.93 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 2 3.62 0.50 120.30 123.92 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 3 3.80 0.50 120.30 124.10 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 3 3.71 0.50 120.30 124.01 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 4 3.66 0.50 120.30 123.96 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 4 3.68 0.50 120.30 123.98 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 5 3.72 0.50 120.30 124.02 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 5 3.74 0.50 120.30 124.04 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 6 3.82 0.50 120.30 124.12 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 6 3.85 0.50 120.30 124.15 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 7 3.62 0.50 120.30 123.92 A A A NE CZ NH1 DAR DAR DAR 2 2 2 N 7 3.77 0.50 120.30 124.07 A A A NE CZ NH2 DAR DAR DAR 5 5 5 N 3 A DIL 6 114.92 -70.67 7 A DIL 6 83.06 75.04 Solution structure of the analogue retro-inverso (MA-S)REGRIGGC in contact with the monoclonal antibody MAB 4X11, NMR, 7 structures 1 N N 2 N N A DAR 2 A DAR 1 HELX_P A GLY 7 A GLY 6 1 1 6 covale 1.345 both A DXX 1 B C DXX 1_555 A DAR 2 A N DAR 1 1_555 covale 1.355 both A DAR 2 A C DAR 1 1_555 A DGL 3 A N DGL 2 1_555 covale 1.342 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 1.356 both A DAR 5 A C DAR 4 1_555 A DIL 6 A N DIL 5 1_555 covale 1.349 both A DIL 6 A C DIL 5 1_555 A GLY 7 A N GLY 6 1_555 covale 1.326 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 1CWZ PDB 1 1CWZ 2 10 1CWZ 2 10 1CWZ 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