1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Skjeldal, L. Gran, L. Sletten, K. Volkman, B.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE 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 LEUCINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US Arch.Biochem.Biophys. ABBIA4 0158 0003-9861 399 142 148 10.1006/abbi.2002.2769 11888199 Refined structure and metal binding site of the kalata B1 peptide. 2002 US Biochemistry BICHAW 0033 0006-2960 34 4147 4158 Elucidation of the Primary and Three-Dimensional Structure of the Uterotonic Polypeptide Kalata B1 1995 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 2917.345 Kalata-B4 1 nat polymer no no NGLPVCGETCVGGTCNTPGCTCSWPVCTR NGLPVCGETCVGGTCNTPGCTCSWPVCTR A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n extracted from plant Oldenlandia sample 1 29 60225 Oldenlandia affinis atom_site entity entity_src_nat pdbx_molecule_features pdbx_nmr_software pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_oper_list pdbx_validate_close_contact pdbx_validate_torsion struct_conn struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Advisory Atomic model Data collection Database references Derived calculations Source and taxonomy Structure summary 1 0 2002-06-12 1 1 2008-04-27 1 2 2011-07-13 2 0 2020-08-12 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_seq_id _atom_site.label_atom_id _entity.pdbx_description _entity_src_nat.pdbx_beg_seq_num _entity_src_nat.pdbx_end_seq_num _pdbx_nmr_software.name _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_torsion.auth_seq_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_seq_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code ELUCIDATION OF THE PRIMARY AND THREE-DIMENSIONAL STRUCTURE OF THE UTEROTONIC POLYPEPTIDE KALATA B1 RCSB Y RCSB 2001-07-10 REL REL Antimicrobial, Antitumor KALATA B1 Cyclic peptide Structure was determined using NOEs from a single 100 ms mixing time NOESY experiment target function 50 20 2D NOESY 0 3 ambient 298 K Structures are based on a total of 333 distance constraints. This includes 6 upper and 6 lower limits defining 3 disulfide bonds, as well as 3 upper and 3 lower limits defining a peptide bond cyclizing the peptide backbone. Residue numbering follows the original description of citation 1, except that for the purposes of structure calculations, the N-terminal residue was taken as Asn8. Therefore, residues 30-36 in this deposition correspond to residues 1-7 in citation 1 and related PDB entry 1kal. Structures were refined in the absence of any artificial constraints defining disulfide bonds until all NOEs had been assigned and low target functions were achieved (tf=0.6). 15 additional calculations were performed with these input data and the inclusion of constraints defining all possible disulfide pairing combinations. The structures containing disulfides between [5(34)-13], [17-29] and [22-27] displayed the lowest target function (0.74, second lowest was 1.54). On the basis of this result and analysis of NOEs observed between Cys sidechain protons, this disulfide bonding arrangement was assumed to be correct and served as the basis for this deposition. torsion angle dynamics 5 mM kalata B1; 90% H2O, 10% D2O 90% H2O/10% D2O P. Guentert refinement DYANA 1.5 Bruker collection XwinNMR 2.6 C. Bartels data analysis XEASY 1.3.11 750 Bruker DMX ASN 8 n 1 ASN 1 A GLY 9 n 2 GLY 2 A LEU 10 n 3 LEU 3 A PRO 11 n 4 PRO 4 A VAL 12 n 5 VAL 5 A CYS 13 n 6 CYS 6 A GLY 14 n 7 GLY 7 A GLU 15 n 8 GLU 8 A THR 16 n 9 THR 9 A CYS 17 n 10 CYS 10 A VAL 18 n 11 VAL 11 A GLY 19 n 12 GLY 12 A GLY 20 n 13 GLY 13 A THR 21 n 14 THR 14 A CYS 22 n 15 CYS 15 A ASN 23 n 16 ASN 16 A THR 24 n 17 THR 17 A PRO 25 n 18 PRO 18 A GLY 26 n 19 GLY 19 A CYS 27 n 20 CYS 20 A THR 28 n 21 THR 21 A CYS 29 n 22 CYS 22 A SER 30 n 23 SER 23 A TRP 31 n 24 TRP 24 A PRO 32 n 25 PRO 25 A VAL 33 n 26 VAL 26 A CYS 34 n 27 CYS 27 A THR 35 n 28 THR 28 A ARG 36 n 29 ARG 29 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 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A N C ASN ARG 1 29 1.37 2 A A N C ASN ARG 1 29 1.37 3 A A H1 C ASN ARG 1 29 1.36 3 A A N C ASN ARG 1 29 1.37 4 A A N C ASN ARG 1 29 1.37 5 A A N C ASN ARG 1 29 1.38 6 A A N C ASN ARG 1 29 1.37 7 A A N C ASN ARG 1 29 1.37 8 A A N C ASN ARG 1 29 1.38 8 A A H O THR THR 21 28 1.59 9 A A N C ASN ARG 1 29 1.38 10 A A N C ASN ARG 1 29 1.38 10 A A H1 C ASN ARG 1 29 1.48 11 A A N C ASN ARG 1 29 1.37 12 A A N C ASN ARG 1 29 1.38 13 A A N C ASN ARG 1 29 1.37 14 A A N C ASN ARG 1 29 1.38 15 A A H1 C ASN ARG 1 29 0.75 15 A A H1 O ASN ARG 1 29 1.29 15 A A N C ASN ARG 1 29 1.31 16 A A N C ASN ARG 1 29 1.38 16 A A O H LEU ARG 3 29 1.59 17 A A N C ASN ARG 1 29 1.36 18 A A N C ASN ARG 1 29 1.38 19 A A N C ASN ARG 1 29 1.36 20 A A N C ASN ARG 1 29 1.37 1 A CYS 10 -154.46 68.76 1 A ASN 16 59.86 16.01 1 A CYS 22 -38.81 114.56 1 A TRP 24 62.46 137.26 2 A CYS 10 -153.93 65.90 2 A ASN 16 82.43 -1.05 2 A CYS 22 -39.93 109.78 2 A TRP 24 62.73 137.62 3 A VAL 5 -142.24 22.82 3 A CYS 10 -153.36 66.70 3 A CYS 22 -38.26 113.32 3 A TRP 24 62.37 136.22 4 A LEU 3 -52.54 109.41 4 A CYS 10 -155.54 62.86 4 A CYS 22 -36.68 112.37 4 A TRP 24 62.59 136.72 5 A VAL 5 -142.39 23.52 5 A CYS 10 -154.28 66.07 5 A ASN 16 84.33 -0.93 5 A CYS 22 -38.29 114.43 5 A TRP 24 62.22 135.97 6 A ASN 16 82.53 -0.93 6 A TRP 24 61.87 138.69 7 A VAL 5 -143.79 20.77 7 A CYS 10 -153.13 68.91 7 A ASN 16 79.26 -0.98 7 A TRP 24 62.16 135.61 8 A CYS 10 -155.93 71.57 8 A CYS 22 -39.59 118.94 8 A TRP 24 62.32 135.27 9 A CYS 10 -152.28 71.63 9 A ASN 16 79.57 -1.20 9 A CYS 22 -37.51 112.53 9 A TRP 24 62.58 136.71 10 A CYS 10 -152.50 74.80 10 A ASN 16 83.27 -1.80 10 A CYS 22 -38.86 114.85 10 A TRP 24 62.65 135.94 11 A VAL 5 -145.10 22.42 11 A CYS 10 -154.59 68.75 11 A CYS 22 -39.05 113.98 11 A TRP 24 62.42 134.26 12 A CYS 10 -155.18 72.58 12 A TRP 24 62.33 135.45 13 A VAL 5 -140.77 24.92 13 A CYS 10 -154.58 71.86 13 A CYS 22 -38.55 118.88 13 A TRP 24 62.43 134.99 14 A VAL 5 -147.84 23.64 14 A CYS 10 -151.81 73.46 14 A ASN 16 80.72 -1.36 14 A CYS 22 -38.55 113.35 14 A TRP 24 62.49 136.38 15 A VAL 5 -144.25 17.19 15 A CYS 10 -156.69 69.16 15 A CYS 22 -24.05 116.55 15 A TRP 24 62.54 137.45 16 A LEU 3 -57.45 109.54 16 A CYS 10 -152.20 74.15 16 A ASN 16 79.61 -1.70 16 A THR 21 -119.74 70.47 16 A CYS 22 -34.50 117.20 16 A TRP 24 62.73 137.02 17 A CYS 10 -151.78 67.43 17 A CYS 22 -38.49 112.82 17 A TRP 24 62.35 136.28 18 A CYS 10 -153.89 72.33 18 A CYS 15 -47.84 165.29 18 A TRP 24 62.14 135.74 19 A CYS 10 -155.94 72.08 19 A CYS 22 -28.56 119.50 19 A TRP 24 62.43 136.67 20 A CYS 10 -150.13 60.53 20 A CYS 22 -26.09 117.36 20 A TRP 24 62.53 138.01 KALATA B1 REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE 1 N N disulf 1.978 A CYS 6 A SG CYS 6 1_555 A CYS 27 A SG CYS 27 1_555 disulf 2.105 A CYS 10 A SG CYS 10 1_555 A CYS 22 A SG CYS 22 1_555 disulf 1.996 A CYS 15 A SG CYS 15 1_555 A CYS 20 A SG CYS 20 1_555 PLANT PROTEIN cyclic peptide, cyclotide, disulfide pairing, uterotonic, PLANT PROTEIN A TRP 24 A TRP 24 1 A PRO 25 A PRO 25 -0.02 A TRP 24 A TRP 24 2 A PRO 25 A PRO 25 0.02 A TRP 24 A TRP 24 3 A PRO 25 A PRO 25 -0.05 A TRP 24 A TRP 24 4 A PRO 25 A PRO 25 -0.04 A TRP 24 A TRP 24 5 A PRO 25 A PRO 25 0.05 A TRP 24 A TRP 24 6 A PRO 25 A PRO 25 -0.01 A TRP 24 A TRP 24 7 A PRO 25 A PRO 25 -0.04 A TRP 24 A TRP 24 8 A PRO 25 A PRO 25 0.01 A TRP 24 A TRP 24 9 A PRO 25 A PRO 25 0.05 A TRP 24 A TRP 24 10 A PRO 25 A PRO 25 0.00 A TRP 24 A TRP 24 11 A PRO 25 A PRO 25 0.07 A TRP 24 A TRP 24 12 A PRO 25 A PRO 25 -0.10 A TRP 24 A TRP 24 13 A PRO 25 A PRO 25 0.02 A TRP 24 A TRP 24 14 A PRO 25 A PRO 25 0.06 A TRP 24 A TRP 24 15 A PRO 25 A PRO 25 0.02 A TRP 24 A TRP 24 16 A PRO 25 A PRO 25 0.01 A TRP 24 A TRP 24 17 A PRO 25 A PRO 25 0.06 A TRP 24 A TRP 24 18 A PRO 25 A PRO 25 -0.01 A TRP 24 A TRP 24 19 A PRO 25 A PRO 25 -0.07 A TRP 24 A TRP 24 20 A PRO 25 A PRO 25 0.03 KAB4_OLDAF UNP 1 1 P83938 GLPVCGETCVGGTCNTPGCTCSWPVCTR 1 28 1JJZ 2 29 P83938 A 1 2 29 1 expression tag ASN 1 1JJZ A P83938 UNP 1