1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Cochran, A.G. Skelton, N.J. Starovasnik, M.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C4 H8 N2 O3 132.118 y ASPARAGINE 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 H15 N2 O2 1 147.195 y LYSINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 98 5578 5583 10.1073/pnas.091100898 11331745 Tryptophan zippers: stable, monomeric beta -hairpins. 2001 To be Published 0353 Chemical-shift-based methods for structure validation and refinement: Application to tryptophan zipper beta-hairpin peptides 10.2210/pdb1le1/pdb pdb_00001le1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 1608.776 Tryptophan Zipper 2 1 syn polymer no yes SWTWENGKWTWK(NH2) SWTWENGKWTWKX A polypeptide(L) n n n n 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 2002-04-24 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _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 2002-04-24 SPRSDE 1LE0 contains Tryptophan Zipper 1 1LE3 contains Tryptophan Zipper 4 RCSB Y PDBJ 2002-04-09 REL This sequence was designed based on experimental data obtained from a model system. The peptide was chemically synthesized and does not appear to occur in nature. sample The structure of trpzip2 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle restraints were derived from analysis of NOESY, ROESY, DQF-COSY, and COSY-35 data. Chi-1 rotamers and stereospecific assignments for beta-methylene groups were based on combined analysis of 3JHaHb and local ROEs, suggesting that all four Trp residues adopt a chi1 of -60 deg. Quantitative analysis of the 1H chemical shifts, however, revealed that the frequencies of the Hb and He3 resonances of Trp4 and Trp11 were inconsistent with a -60 deg chi1 value, and indicated that the side chains for these tryptophans actually reside primarily in the 180 deg chi1 rotamer (Skelton et al., manuscript in preparation). The current coordinates result from refinement with the Sander module of AMBER (v6.0), and included not only NOE-derived distance restraints and dihedral angle restraints, but also 1H chemical shift-based restraints. Thus, the resulting updated coordinates differ from the previous ones in the side chain orientations of Trp4 and Trp11. However, the rest of the structure is similar with a backbone rmsd between the average coordinates of the two ensembles of 0.69 angstrom(res.2-11). The two strands are highly twisted, as described previously, however there is a slight difference in the relative position of the turn with respect to the strands. The key difference, however, is that each pair of cross-strand tryptophan rings now shows edge-to-face packing against one another. structures with the least restraint violations 76 20 2D NOESY DQF-COSY 2D TOCSY 2D ROESY 2D COSY-35 0 5.5 ambient 288 K Structures are based on a total of 80 (including 26 intra-residue, 15 sequential, 6 medium-range, and 33 long-range) NOE-derived distance restraints, 15 dihedral angle restraints, and 1H chemical shift restraints for 39 carbon-bound 1H resonances; (chemical shift restraints were not imposed for the terminal residues, or for side chains exhibiting evidence of rotational averaging). The ensemble agrees well with the experimental restraints with no distance or dihedral angle violations greater than 0.10 angstrom or 5 deg, respectively, and an average rmsd of only 0.087 ppm between observed and calculated chemical shifts. Hybrid distance geometry/simulated annealing using the program DGII, followed by molecular dynamics using the program AMBER, in conjunction not only with distance and dihedral angle restraints, but also 1H chemical shift-based restraints. 1 closest to the average 3mM trpzip2 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS Bruker collection XwinNMR 2.5 Molecular Simulations, Inc. data analysis Felix 98.0 Molecular Simulations, Inc. structure solution DGII 98.0 Case and Kollman refinement Amber 6.0 500 Bruker DRX SER 1 n 1 SER 1 A TRP 2 n 2 TRP 2 A THR 3 n 3 THR 3 A TRP 4 n 4 TRP 4 A GLU 5 n 5 GLU 5 A ASN 6 n 6 ASN 6 A GLY 7 n 7 GLY 7 A LYS 8 n 8 LYS 8 A TRP 9 n 9 TRP 9 A THR 10 n 10 THR 10 A TRP 11 n 11 TRP 11 A LYS 12 n 12 LYS 12 A NH2 13 n 13 NH2 13 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 A N THR 3 A N THR 3 A O THR 10 A O THR 10 8 A A HG O SER LYS 1 12 1.52 14 A A HG O SER LYS 1 12 1.54 1 A ASN 6 31.17 71.16 2 A ASN 6 29.80 62.76 4 A ASN 6 50.22 18.78 6 A ASN 6 41.60 28.30 8 A ASN 6 33.33 44.79 9 A ASN 6 34.84 68.84 10 A ASN 6 34.40 51.77 11 A ASN 6 38.01 55.10 12 A ASN 6 45.94 24.55 13 A ASN 6 38.37 71.61 14 A ASN 6 27.47 72.00 15 A ASN 6 45.07 20.80 16 A ASN 6 29.31 61.79 17 A TRP 2 -57.39 106.81 17 A ASN 6 31.54 65.53 19 A ASN 6 29.23 72.24 20 A ASN 6 29.15 65.91 NMR Structure of Tryptophan Zipper 2: A stable, Monomeric Beta-Hairpin with a Type I' Turn 1 Y N covale 1.324 both A LYS 12 A C LYS 12 1_555 A NH2 13 A N NH2 13 1_555 DE NOVO PROTEIN beta-hairpin, type I' turn, DE NOVO PROTEIN 1LE1 PDB 1 1LE1 1 13 1LE1 1 13 1LE1 A 1 1 13 2 anti-parallel A TRP 2 A TRP 2 A GLU 5 A GLU 5 A LYS 8 A LYS 8 A TRP 11 A TRP 11 BINDING SITE FOR RESIDUE NH2 A 13 A NH2 13 Software 1 A LYS 12 A LYS 12 1 1_555