1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Tietz, J.I. Schwalen, C.J. Blair, P.M. Zakai, U.I. Mitchell, D.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID 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 C9 H11 N O2 165.189 y PHENYLALANINE 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N C N 7 N C N 8 N N N 9 N C N 10 N N N 11 N N N 12 N O N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N N N 29 S C N 30 N C N 31 N O N 32 N C N 33 N C N 34 N O N 35 N N N 36 N O N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N N N 46 S C N 47 N C N 48 N O N 49 N C N 50 N C N 51 N O N 52 N O N 53 N O N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N N N 62 R C N 63 N C N 64 N O N 65 N C N 66 N S N 67 N O N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N N N 76 S C N 77 N C N 78 N O N 79 N C N 80 N C N 81 N C N 82 N O N 83 N O N 84 N O N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 N C N 96 N C N 97 N O N 98 N O N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N N N 105 S C N 106 N C N 107 N O N 108 N C Y 109 N C Y 110 N C Y 111 N C Y 112 N C Y 113 N C Y 114 N C N 115 N O N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 S C N 129 N C N 130 N O N 131 N C N 132 N C N 133 N C N 134 N O N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N N N 145 S C N 146 N C N 147 N O N 148 N C N 149 N O N 150 N O N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N N N 159 S C N 160 N C N 161 N O N 162 N C Y 163 N C Y 164 N C Y 165 N C Y 166 N N Y 167 N C Y 168 N C Y 169 N C Y 170 N C Y 171 N C N 172 N O N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N N N 186 S C N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C N 192 N O N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N doub N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N doub N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N doub N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N doub N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing Y 109 N doub Y 110 N sing Y 111 N sing N 112 N sing Y 113 N doub N 114 N sing Y 115 N doub N 116 N sing Y 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub N 158 N sing N 159 N sing N 160 N sing N 161 N sing Y 162 N doub Y 163 N sing Y 164 N sing N 165 N sing Y 166 N doub Y 167 N sing Y 168 N sing N 169 N sing Y 170 N sing Y 171 N doub N 172 N sing Y 173 N doub N 174 N sing Y 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N doub N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing US Nat. Chem. Biol. 1552-4469 13 470 478 10.1038/nchembio.2319 28244986 A new genome-mining tool redefines the lasso peptide biosynthetic landscape. 2017 10.2210/pdb5jpl/pdb pdb_00005jpl 10.13018/BMR30073 2027.247 Uncharacterized protein residues 30-46 1 nat polymer no no GRPNWGFENDWSCVRVC GRPNWGFENDWSCVRVC A polypeptide(L) n n n n n n n n n n n n n n n n n sample 1 17 1205910 Nocardiopsis alba (strain ATCC BAA-2165 / BE74) USDA-ARS NRRL Collection ATCC BAA-2165 / BE74 atom_site database_2 pdbx_nmr_software pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact struct_conn struct_conn_type pdbx_database_status chem_comp_atom chem_comp_bond database_2 pdbx_entry_details pdbx_modification_feature repository Initial release Database references Database references Advisory Atomic model Data collection Database references Derived calculations Other Data collection Database references Structure summary 1 0 2017-03-01 1 1 2017-03-15 1 2 2017-04-26 2 0 2022-11-30 2 1 2023-06-14 2 2 2024-11-20 _atom_site.auth_atom_id _atom_site.label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_database_status.status_code_nmr_data _database_2.pdbx_DOI N RCSB Y RCSB 2016-05-03 REL REL REL REL Y A CYS 13 Disulfide bridge SG A CYS 13 A CYS 17 SG A CYS 17 1_555 1_555 None structures with the lowest energy 200 20 anisotropic 1 1H anisotropic 1 2D 1H-1H NOESY anisotropic 1 2D 1H-13C HSQC aliphatic anisotropic 1 2D 1H-13C HSQC aromatic anisotropic 1 2D 1H-1H TOCSY 5 mM none room temperature 1 Not defined conditions 7 Not defined 1 atm 298 K simulated annealing 1 lowest energy 5 mM LP2006, methanol Natural product dissolved in CD3OH. CD3OH_sample methanol solution Charles Schwieters, Marius Clore (NIH) refinement XPLOR-NIH 2.36 Bruker Biospin collection TopSpin 1.3 Mestrelab Research chemical shift assignment MestReNova 8.1.1 Goddard peak picking Sparky Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Charles Schwieters, Marius Clore (NIH) structure calculation XPLOR-NIH 2.36 inverse 5 mm TCI cryogenic probe with z-axis pulsed field gradient (pfg) capability 900 Bruker AVANCE GLY 1 n 1 GLY 1 A ARG 2 n 2 ARG 2 A PRO 3 n 3 PRO 3 A ASN 4 n 4 ASN 4 A TRP 5 n 5 TRP 5 A GLY 6 n 6 GLY 6 A PHE 7 n 7 PHE 7 A GLU 8 n 8 GLU 8 A ASN 9 n 9 ASN 9 A ASP 10 n 10 ASP 10 A TRP 11 n 11 TRP 11 A SER 12 n 12 SER 12 A CYS 13 n 13 CYS 13 A VAL 14 n 14 VAL 14 A ARG 15 n 15 ARG 15 A VAL 16 n 16 VAL 16 A CYS 17 n 17 CYS 17 A author_defined_assembly 1 monomeric 0 0 1730 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 A N ARG 2 A N ARG 2 A O CYS 13 A O CYS 13 1 A OE2 GLU 8 A OE2 GLU 8 1 Y 2 A OE2 GLU 8 A OE2 GLU 8 1 Y 3 A OE2 GLU 8 A OE2 GLU 8 1 Y 4 A OE2 GLU 8 A OE2 GLU 8 1 Y 5 A OE2 GLU 8 A OE2 GLU 8 1 Y 6 A OE2 GLU 8 A OE2 GLU 8 1 Y 7 A OE2 GLU 8 A OE2 GLU 8 1 Y 8 A OE2 GLU 8 A OE2 GLU 8 1 Y 9 A OE2 GLU 8 A OE2 GLU 8 1 Y 10 A OE2 GLU 8 A OE2 GLU 8 1 Y 11 A OE2 GLU 8 A OE2 GLU 8 1 Y 12 A OE2 GLU 8 A OE2 GLU 8 1 Y 13 A OE2 GLU 8 A OE2 GLU 8 1 Y 14 A OE2 GLU 8 A OE2 GLU 8 1 Y 15 A OE2 GLU 8 A OE2 GLU 8 1 Y 16 A OE2 GLU 8 A OE2 GLU 8 1 Y 17 A OE2 GLU 8 A OE2 GLU 8 1 Y 18 A OE2 GLU 8 A OE2 GLU 8 1 Y 19 A OE2 GLU 8 A OE2 GLU 8 1 Y 20 A OE2 GLU 8 A OE2 GLU 8 1 Y 1 A A N CD GLY GLU 1 8 1.33 2 A A HD21 H ASN TRP 9 11 1.25 2 A A N CD GLY GLU 1 8 1.33 3 A A N CD GLY GLU 1 8 1.33 4 A A HD21 H ASN TRP 9 11 1.22 4 A A N CD GLY GLU 1 8 1.34 5 A A N CD GLY GLU 1 8 1.34 6 A A N CD GLY GLU 1 8 1.34 7 A A N CD GLY GLU 1 8 1.34 8 A A N CD GLY GLU 1 8 1.34 8 A A H1 OG GLY SER 1 12 1.56 9 A A HD21 H ASN TRP 9 11 1.28 9 A A N CD GLY GLU 1 8 1.33 10 A A N CD GLY GLU 1 8 1.33 11 A A HD21 H ASN TRP 9 11 1.25 11 A A N CD GLY GLU 1 8 1.34 12 A A N CD GLY GLU 1 8 1.34 13 A A N CD GLY GLU 1 8 1.34 14 A A HD21 H ASN TRP 9 11 1.23 14 A A N CD GLY GLU 1 8 1.33 15 A A N CD GLY GLU 1 8 1.33 16 A A N CD GLY GLU 1 8 1.34 17 A A N CD GLY GLU 1 8 1.34 18 A A HD21 H ASN TRP 9 11 1.28 18 A A HD22 HG ASN SER 9 12 1.30 18 A A N CD GLY GLU 1 8 1.34 19 A A N CD GLY GLU 1 8 1.33 20 A A HD21 H ASN TRP 9 11 1.25 20 A A N CD GLY GLU 1 8 1.33 1 A ASN 4 175.62 21.30 1 A PHE 7 -136.75 -41.84 1 A ASN 9 40.07 15.35 1 A VAL 16 55.45 -86.49 2 A PRO 3 -45.36 83.35 2 A ASN 4 -172.69 34.01 2 A TRP 5 53.55 107.22 2 A ASN 9 41.82 17.59 2 A ASP 10 48.87 11.90 3 A ARG 2 -38.71 102.04 3 A PRO 3 -45.41 100.20 3 A ASN 4 -172.89 23.92 3 A TRP 5 51.50 104.22 3 A ASN 9 42.06 16.06 3 A ASP 10 47.06 22.85 3 A TRP 11 -144.50 10.38 3 A ARG 15 -142.53 -72.06 4 A ARG 2 -174.94 104.09 4 A PRO 3 -44.53 86.03 4 A ASN 4 -159.62 28.58 4 A TRP 5 47.63 91.20 4 A ASN 9 41.80 13.88 4 A ASP 10 54.46 0.00 4 A VAL 14 -90.97 -156.92 5 A PRO 3 -64.98 99.85 5 A ASN 4 -174.98 -128.77 5 A TRP 5 -161.48 99.72 5 A ASN 9 46.70 12.53 5 A ASP 10 43.07 19.32 5 A TRP 11 -154.79 19.15 5 A ARG 15 -140.77 -84.87 6 A PRO 3 -45.26 85.96 6 A ASN 4 -160.55 32.58 6 A TRP 5 54.26 96.26 6 A PHE 7 -80.35 -79.82 6 A GLU 8 -48.33 161.57 6 A ASN 9 55.61 7.66 6 A ASP 10 57.83 9.90 6 A TRP 11 -160.16 29.71 7 A ASN 4 76.10 155.58 7 A PHE 7 -87.07 -83.74 7 A GLU 8 -44.02 159.81 7 A ASN 9 53.88 12.20 7 A ASP 10 57.57 7.91 7 A TRP 11 -159.34 35.65 7 A VAL 14 -67.55 -143.52 8 A ASN 4 83.36 114.40 8 A TRP 5 -37.82 120.94 8 A PHE 7 -80.82 -73.73 8 A GLU 8 -49.41 152.78 8 A ASN 9 54.24 8.82 8 A ASP 10 55.75 5.09 8 A TRP 11 -142.66 21.23 8 A ARG 15 -145.03 -65.07 9 A PRO 3 -41.12 172.70 9 A ASN 4 58.30 121.58 9 A ASN 9 40.98 17.63 9 A ASP 10 46.25 15.40 9 A ARG 15 -167.68 -51.31 10 A TRP 5 -32.89 141.06 10 A ASN 9 46.38 18.46 10 A ASP 10 51.45 11.65 10 A TRP 11 -159.45 37.60 11 A PRO 3 -40.55 179.26 11 A ASN 4 79.20 98.22 11 A TRP 5 -35.53 121.94 11 A PHE 7 -93.64 -68.08 11 A ASN 9 41.31 18.82 11 A ASP 10 45.84 13.31 11 A VAL 14 -97.26 -118.79 12 A PRO 3 -54.20 -162.20 12 A ASN 4 60.41 113.16 12 A PHE 7 -90.97 -70.80 12 A GLU 8 -49.67 150.92 12 A ASN 9 55.57 6.20 12 A TRP 11 -146.86 26.85 13 A ASN 4 90.13 110.21 13 A ASN 9 56.33 5.22 13 A ASP 10 62.19 -0.12 13 A VAL 14 -77.06 -92.18 14 A ASN 4 -173.72 17.26 14 A PHE 7 -154.10 -19.25 14 A GLU 8 -59.10 -103.09 14 A ASN 9 -70.18 38.80 14 A ASP 10 43.79 21.72 14 A TRP 11 -152.06 8.44 15 A ASN 4 -174.41 -121.15 15 A TRP 5 -175.64 102.53 15 A PHE 7 -159.68 -60.48 15 A ASN 9 53.61 8.64 15 A TRP 11 -157.42 9.96 15 A ARG 15 42.94 -129.26 16 A ASN 4 -155.50 25.99 16 A TRP 5 47.57 98.53 16 A ASN 9 55.03 6.74 16 A ASP 10 57.88 2.75 16 A ARG 15 -157.48 -38.07 17 A ASN 4 -64.59 -169.39 17 A PHE 7 -99.23 -67.56 17 A GLU 8 -53.84 176.34 17 A ASN 9 48.43 16.20 17 A ASP 10 69.56 -10.04 17 A TRP 11 -166.43 73.14 17 A SER 12 -171.28 144.87 18 A PRO 3 -42.06 98.70 18 A ASN 4 -173.00 31.17 18 A TRP 5 44.02 88.63 18 A PHE 7 -94.33 -66.20 18 A ASN 9 43.14 15.57 18 A ASP 10 46.65 14.46 18 A VAL 14 -71.08 -96.32 18 A VAL 16 53.53 107.88 19 A PRO 3 -70.12 25.46 19 A TRP 5 -25.37 125.37 19 A ASN 9 41.62 16.61 19 A ASP 10 49.41 17.57 19 A TRP 11 -140.26 10.77 19 A VAL 14 -72.00 -123.20 20 A ARG 2 -38.38 102.63 20 A PRO 3 -46.00 102.35 20 A ASN 4 -179.83 23.61 20 A TRP 5 48.52 106.36 20 A PHE 7 -146.67 -35.76 20 A GLU 8 -47.09 -105.65 20 A ASN 9 -75.17 29.36 20 A ASP 10 56.33 -1.06 N LP2006, a handcuff-topology lasso peptide antibiotic 1 N N A PHE 7 A PHE 7 HELX_P A ASP 10 A ASP 10 5 AA1 4 disulf 2.018 A CYS 13 A SG CYS 13 1_555 A CYS 17 A SG CYS 17 1_555 ANTIBIOTIC lasso peptide, RiPP, antibiotic macrocyclic, ANTIBIOTIC J7LF03_NOCAA UNP 1 30 J7LF03 GRPNWGFENDWSCVRVC 30 46 5JPL 1 17 J7LF03 A 1 1 17 2 anti-parallel A ARG 2 A ARG 2 A PRO 3 A PRO 3 A SER 12 A SER 12 A CYS 13 A CYS 13