data_6O57 # _model_server_result.job_id cp2eCLBojn8nG_mmnp6kgw _model_server_result.datetime_utc '2024-11-27 20:11:32' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6o57 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 6O57 # _exptl.entry_id 6O57 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 770.983 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6O57 _cell.length_a 54.881 _cell.length_b 54.881 _cell.length_c 82.131 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O57 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C35 H68 N11 O8 1' _chem_comp.formula_weight 770.983 _chem_comp.id 2NC _chem_comp.mon_nstd_flag . _chem_comp.name N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms p2/NC # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C O 2NC doub 1 n n C CH3 2NC sing 2 n n CH3 H1 2NC sing 3 n n CH3 H2 2NC sing 4 n n CH3 H3 2NC sing 5 n n N CA 2NC sing 6 n n N H 2NC sing 7 n n CA C1 2NC sing 8 n n CA CB 2NC sing 9 n n CA HA 2NC sing 10 n n C1 O1 2NC doub 11 n n CB OG1 2NC sing 12 n n CB CG2 2NC sing 13 n n CB HB 2NC sing 14 n n OG1 HG1 2NC sing 15 n n CG2 HG21 2NC sing 16 n n CG2 HG22 2NC sing 17 n n CG2 HG23 2NC sing 18 n n N1 CA1 2NC sing 19 n n N1 H4 2NC sing 20 n n CA1 C2 2NC sing 21 n n CA1 CB1 2NC sing 22 n n CA1 HA1 2NC sing 23 n n C2 O2 2NC doub 24 n n CB1 CG1 2NC sing 25 n n CB1 CG21 2NC sing 26 n n CB1 HB1 2NC sing 27 n n CG1 CD1 2NC sing 28 n n CG1 HG12 2NC sing 29 n n CG1 HG13 2NC sing 30 n n CG21 HG24 2NC sing 31 n n CG21 HG25 2NC sing 32 n n CG21 HG26 2NC sing 33 n n CD1 HD11 2NC sing 34 n n CD1 HD12 2NC sing 35 n n CD1 HD13 2NC sing 36 n n N2 CA2 2NC sing 37 n n N2 H5 2NC sing 38 n n CA2 C3 2NC sing 39 n n CA2 CB2 2NC sing 40 n n CA2 HA2 2NC sing 41 n n CB2 CG 2NC sing 42 n n CB2 HB2 2NC sing 43 n n CB2 HB3 2NC sing 44 n n CG CD 2NC sing 45 n n CG HG2 2NC sing 46 n n CG HG3 2NC sing 47 n n CD CE 2NC sing 48 n n CD HD2 2NC sing 49 n n CD HD3 2NC sing 50 n n CE HE1 2NC sing 51 n n CE HE2 2NC sing 52 n n CE HE3 2NC sing 53 n n N3 CA3 2NC sing 54 n n N3 H6 2NC sing 55 n n CA3 C4 2NC sing 56 n n CA3 CB3 2NC sing 57 n n CA3 HA3 2NC sing 58 n n C4 O3 2NC doub 59 n n CB3 CG3 2NC sing 60 n n CB3 HB21 2NC sing 61 n n CB3 HB31 2NC sing 62 n n CG3 CD2 2NC sing 63 n n CG3 HG27 2NC sing 64 n n CG3 HG31 2NC sing 65 n n CD2 CE1 2NC sing 66 n n CD2 HD21 2NC sing 67 n n CD2 HD31 2NC sing 68 n n CE1 HE11 2NC sing 69 n n CE1 HE21 2NC sing 70 n n CE1 HE31 2NC sing 71 n n N4 CA4 2NC sing 72 n n N4 H7 2NC sing 73 n n CA4 C5 2NC sing 74 n n CA4 CB4 2NC sing 75 n n CA4 HA4 2NC sing 76 n n C5 O4 2NC doub 77 n n CB4 CG4 2NC sing 78 n n CB4 HB22 2NC sing 79 n n CB4 HB32 2NC sing 80 n n CG4 CD3 2NC sing 81 n n CG4 HG28 2NC sing 82 n n CG4 HG32 2NC sing 83 n n CD3 OE1 2NC doub 84 n n CD3 NE2 2NC sing 85 n n NE2 HE22 2NC sing 86 n n NE2 HE23 2NC sing 87 n n N5 CA5 2NC sing 88 n n N5 H8 2NC sing 89 n n CA5 C6 2NC sing 90 n n CA5 CB5 2NC sing 91 n n CA5 HA5 2NC sing 92 n n C6 O5 2NC doub 93 n n CB5 CG5 2NC sing 94 n n CB5 HB23 2NC sing 95 n n CB5 HB33 2NC sing 96 n n CG5 CD4 2NC sing 97 n n CG5 HG29 2NC sing 98 n n CG5 HG33 2NC sing 99 n n CD4 NE 2NC sing 100 n n CD4 HD22 2NC sing 101 n n CD4 HD32 2NC sing 102 n n NE CZ 2NC sing 103 n n NE HE 2NC sing 104 n n CZ NH1 2NC sing 105 n n CZ NH2 2NC doub 106 n n NH1 HH11 2NC sing 107 n n NH1 HH12 2NC sing 108 n n NH2 HH21 2NC sing 109 n n NH2 HH22 2NC sing 110 n n N6 HN1 2NC sing 111 n n N6 HN2 2NC sing 112 n n C N 2NC sing 113 n n C1 N1 2NC sing 114 n n C2 N2 2NC sing 115 n n C3 N3 2NC sing 116 n n C4 N4 2NC sing 117 n n C5 N5 2NC sing 118 n n C3 HC31 2NC sing 119 n n C3 HC32 2NC sing 120 n n C6 N6 2NC sing 121 n n # _atom_sites.entry_id 6O57 _atom_sites.fract_transf_matrix[1][1] 0.018221 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018221 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012176 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 FMT A 1 101 541 FMT FMT . D 3 2NC B 1 201 201 2NC 2NC . E 2 FMT B 1 202 542 FMT FMT . F 2 FMT B 1 203 543 FMT FMT . G 2 FMT B 1 204 544 FMT FMT . H 4 HOH A 1 201 1002 HOH HOH . H 4 HOH A 2 202 1049 HOH HOH . H 4 HOH A 3 203 1056 HOH HOH . H 4 HOH A 4 204 1043 HOH HOH . H 4 HOH A 5 205 1022 HOH HOH . H 4 HOH A 6 206 1033 HOH HOH . H 4 HOH A 7 207 1023 HOH HOH . H 4 HOH A 8 208 1025 HOH HOH . H 4 HOH A 9 209 1045 HOH HOH . H 4 HOH A 10 210 1096 HOH HOH . H 4 HOH A 11 211 1024 HOH HOH . H 4 HOH A 12 212 1046 HOH HOH . H 4 HOH A 13 213 1006 HOH HOH . H 4 HOH A 14 214 1076 HOH HOH . H 4 HOH A 15 215 1034 HOH HOH . H 4 HOH A 16 216 1091 HOH HOH . H 4 HOH A 17 217 1055 HOH HOH . H 4 HOH A 18 218 1004 HOH HOH . H 4 HOH A 19 219 1038 HOH HOH . H 4 HOH A 20 220 1036 HOH HOH . H 4 HOH A 21 221 1028 HOH HOH . H 4 HOH A 22 222 1110 HOH HOH . H 4 HOH A 23 223 1097 HOH HOH . H 4 HOH A 24 224 1018 HOH HOH . H 4 HOH A 25 225 1011 HOH HOH . H 4 HOH A 26 226 1047 HOH HOH . H 4 HOH A 27 227 1116 HOH HOH . H 4 HOH A 28 228 1044 HOH HOH . H 4 HOH A 29 229 1014 HOH HOH . H 4 HOH A 30 230 1039 HOH HOH . H 4 HOH A 31 231 1111 HOH HOH . H 4 HOH A 32 232 1032 HOH HOH . H 4 HOH A 33 233 1051 HOH HOH . H 4 HOH A 34 234 1102 HOH HOH . H 4 HOH A 35 235 1103 HOH HOH . H 4 HOH A 36 236 1077 HOH HOH . H 4 HOH A 37 237 1037 HOH HOH . H 4 HOH A 38 238 1057 HOH HOH . H 4 HOH A 39 239 1113 HOH HOH . I 4 HOH B 1 301 1114 HOH HOH . I 4 HOH B 2 302 1030 HOH HOH . I 4 HOH B 3 303 1108 HOH HOH . I 4 HOH B 4 304 1093 HOH HOH . I 4 HOH B 5 305 1053 HOH HOH . I 4 HOH B 6 306 1013 HOH HOH . I 4 HOH B 7 307 1080 HOH HOH . I 4 HOH B 8 308 1001 HOH HOH . I 4 HOH B 9 309 1027 HOH HOH . I 4 HOH B 10 310 1068 HOH HOH . I 4 HOH B 11 311 1090 HOH HOH . I 4 HOH B 12 312 1067 HOH HOH . I 4 HOH B 13 313 1107 HOH HOH . I 4 HOH B 14 314 1008 HOH HOH . I 4 HOH B 15 315 1072 HOH HOH . I 4 HOH B 16 316 1069 HOH HOH . I 4 HOH B 17 317 1005 HOH HOH . I 4 HOH B 18 318 1079 HOH HOH . I 4 HOH B 19 319 1092 HOH HOH . I 4 HOH B 20 320 1003 HOH HOH . I 4 HOH B 21 321 1052 HOH HOH . I 4 HOH B 22 322 1065 HOH HOH . I 4 HOH B 23 323 1112 HOH HOH . I 4 HOH B 24 324 1094 HOH HOH . I 4 HOH B 25 325 1009 HOH HOH . I 4 HOH B 26 326 1073 HOH HOH . I 4 HOH B 27 327 1010 HOH HOH . I 4 HOH B 28 328 1082 HOH HOH . I 4 HOH B 29 329 1066 HOH HOH . I 4 HOH B 30 330 1085 HOH HOH . I 4 HOH B 31 331 1016 HOH HOH . I 4 HOH B 32 332 1061 HOH HOH . I 4 HOH B 33 333 1104 HOH HOH . I 4 HOH B 34 334 1109 HOH HOH . I 4 HOH B 35 335 1070 HOH HOH . I 4 HOH B 36 336 1115 HOH HOH . I 4 HOH B 37 337 1083 HOH HOH . I 4 HOH B 38 338 1060 HOH HOH . I 4 HOH B 39 339 1059 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C 2NC . . . D 3 73.048 21.537 10.618 1 36.04 ? C 2NC 201 B 1 HETATM 2 O O 2NC . . . D 3 71.833 21.688 10.819 1 34.29 ? O 2NC 201 B 1 HETATM 3 C CH3 2NC . . . D 3 74.116 22.066 11.501 1 33.83 ? CH3 2NC 201 B 1 HETATM 4 N N 2NC . . . D 3 73.661 20.793 9.655 1 37.26 ? N 2NC 201 B 1 HETATM 5 C CA 2NC . . . D 3 72.895 20.217 8.657 1 38.51 ? CA 2NC 201 B 1 HETATM 6 C C1 2NC . . . D 3 72.548 18.755 9.057 1 38.27 ? C1 2NC 201 B 1 HETATM 7 O O1 2NC . . . D 3 73.346 17.774 9.246 1 33.81 ? O1 2NC 201 B 1 HETATM 8 C CB 2NC . . . D 3 73.576 20.334 7.227 1 36.48 ? CB 2NC 201 B 1 HETATM 9 O OG1 2NC . . . D 3 73.765 21.684 6.768 1 42.71 ? OG1 2NC 201 B 1 HETATM 10 C CG2 2NC . . . D 3 72.588 19.746 6.287 1 41.68 ? CG2 2NC 201 B 1 HETATM 11 N N1 2NC . . . D 3 71.388 18.443 9.169 1 34.67 ? N1 2NC 201 B 1 HETATM 12 C CA1 2NC . . . D 3 70.931 17.112 9.418 1 31.47 ? CA1 2NC 201 B 1 HETATM 13 C C2 2NC . . . D 3 70.006 16.417 8.472 1 37.64 ? C2 2NC 201 B 1 HETATM 14 O O2 2NC . . . D 3 68.75 16.567 8.262 1 34.18 ? O2 2NC 201 B 1 HETATM 15 C CB1 2NC . . . D 3 70.29 17.135 10.804 1 32.19 ? CB1 2NC 201 B 1 HETATM 16 C CG1 2NC . . . D 3 70.815 18.076 11.924 1 32.79 ? CG1 2NC 201 B 1 HETATM 17 C CG21 2NC . . . D 3 69.927 15.801 11.271 1 37.01 ? CG21 2NC 201 B 1 HETATM 18 C CD1 2NC . . . D 3 72.31 17.833 12.325 1 31.77 ? CD1 2NC 201 B 1 HETATM 19 N N2 2NC . . . D 3 70.53 15.664 7.824 1 34.69 ? N2 2NC 201 B 1 HETATM 20 C CA2 2NC . . . D 3 69.741 15.071 6.764 1 35.21 ? CA2 2NC 201 B 1 HETATM 21 C C3 2NC . . . D 3 69.084 13.703 6.888 1 32.26 ? C3 2NC 201 B 1 HETATM 22 C CB2 2NC . . . D 3 70.312 15.174 5.389 1 41.06 ? CB2 2NC 201 B 1 HETATM 23 C CG 2NC . . . D 3 71.118 16.415 5.141 1 41.6 ? CG 2NC 201 B 1 HETATM 24 C CD 2NC . . . D 3 70.601 17.505 4.364 1 46.48 ? CD 2NC 201 B 1 HETATM 25 C CE 2NC . . . D 3 69.326 17.23 3.595 1 50.01 ? CE 2NC 201 B 1 HETATM 26 N N3 2NC . . . D 3 68.58 13.343 8.199 1 34.08 ? N3 2NC 201 B 1 HETATM 27 C CA3 2NC . . . D 3 67.483 12.365 8.292 1 33.95 ? CA3 2NC 201 B 1 HETATM 28 C C4 2NC . . . D 3 66.474 12.506 7.244 1 32.08 ? C4 2NC 201 B 1 HETATM 29 O O3 2NC . . . D 3 65.794 13.535 6.825 1 32.8 ? O3 2NC 201 B 1 HETATM 30 C CB3 2NC . . . D 3 66.919 12.449 9.646 1 38.19 ? CB3 2NC 201 B 1 HETATM 31 C CG3 2NC . . . D 3 66.133 11.212 9.998 1 41.28 ? CG3 2NC 201 B 1 HETATM 32 C CD2 2NC . . . D 3 64.836 11.721 10.446 1 43.96 ? CD2 2NC 201 B 1 HETATM 33 C CE1 2NC . . . D 3 65.029 12.634 11.645 1 50.7 ? CE1 2NC 201 B 1 HETATM 34 N N4 2NC . . . D 3 66.098 11.49 6.714 1 31.78 ? N4 2NC 201 B 1 HETATM 35 C CA4 2NC . . . D 3 64.977 11.483 5.751 1 29.29 ? CA4 2NC 201 B 1 HETATM 36 C C5 2NC . . . D 3 64.034 10.265 5.925 1 34.15 ? C5 2NC 201 B 1 HETATM 37 O O4 2NC . . . D 3 64.466 8.963 5.958 1 32.04 ? O4 2NC 201 B 1 HETATM 38 C CB4 2NC . . . D 3 65.403 11.861 4.306 1 31.68 ? CB4 2NC 201 B 1 HETATM 39 C CG4 2NC . . . D 3 64.322 11.795 3.258 1 32.58 ? CG4 2NC 201 B 1 HETATM 40 C CD3 2NC . . . D 3 64.108 10.454 2.716 1 37.58 ? CD3 2NC 201 B 1 HETATM 41 O OE1 2NC . . . D 3 64.821 9.574 2.877 1 38.93 ? OE1 2NC 201 B 1 HETATM 42 N NE2 2NC . . . D 3 62.963 10.281 2.058 1 41.73 ? NE2 2NC 201 B 1 HETATM 43 N N5 2NC . . . D 3 62.798 10.341 5.777 1 40.03 ? N5 2NC 201 B 1 HETATM 44 C CA5 2NC . . . D 3 61.864 9.101 5.697 1 36.86 ? CA5 2NC 201 B 1 HETATM 45 C C6 2NC . . . D 3 60.879 9.262 4.622 1 38.34 ? C6 2NC 201 B 1 HETATM 46 O O5 2NC . . . D 3 60.587 10.42 4.316 1 33.71 ? O5 2NC 201 B 1 HETATM 47 C CB5 2NC . . . D 3 61.211 9.207 7.025 1 42.03 ? CB5 2NC 201 B 1 HETATM 48 C CG5 2NC . . . D 3 62.03 8.727 8.169 1 39.08 ? CG5 2NC 201 B 1 HETATM 49 C CD4 2NC . . . D 3 60.908 8.636 9.121 1 45.17 ? CD4 2NC 201 B 1 HETATM 50 N NE 2NC . . . D 3 61.608 8.273 10.407 1 47.86 ? NE 2NC 201 B 1 HETATM 51 C CZ 2NC . . . D 3 61.102 8.281 11.637 1 47.77 ? CZ 2NC 201 B 1 HETATM 52 N NH1 2NC . . . D 3 59.87 8.68 11.912 1 46.08 ? NH1 2NC 201 B 1 HETATM 53 N NH2 2NC . . . D 3 61.889 7.881 12.645 1 48.14 ? NH2 2NC 201 B 1 HETATM 54 N N6 2NC . . . D 3 60.318 8.286 3.829 1 36.71 ? N6 2NC 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 54 #