data_6KK5 # _model_server_result.job_id 32H5jyocySUtFEikypF23w _model_server_result.datetime_utc '2024-11-08 20:54:46' _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 6kk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 6KK5 # _exptl.entry_id 6KK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 644.809 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(5~{S},8~{R},15~{S},18~{S})-15,18-bis(4-azanylbutyl)-5-methyl-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine _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 6KK5 _cell.length_a 42.528 _cell.length_b 42.528 _cell.length_c 215.371 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _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 _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 144 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 143 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 144 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 143 _struct_conn.ptnr2_symmetry 8_444 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.126 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C31 H52 N10 O5' _chem_comp.formula_weight 644.809 _chem_comp.id DE6 _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(5~{S},8~{R},15~{S},18~{S})-15,18-bis(4-azanylbutyl)-5-methyl-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N14 C12 DE6 doub 83 n n N11 C12 DE6 sing 84 n n N11 C10 DE6 sing 85 n n C12 N13 DE6 sing 86 n n N08 C06 DE6 sing 87 n n N08 C09 DE6 sing 88 n n C06 C07 DE6 sing 89 n n C06 C05 DE6 sing 90 n n C15 C10 DE6 sing 91 n n C15 C16 DE6 sing 92 n n N04 C05 DE6 sing 93 n n N04 C03 DE6 sing 94 n n C10 C09 DE6 sing 95 n n C05 O46 DE6 doub 96 n n C09 O45 DE6 doub 97 n n C17 C16 DE6 sing 98 n n C17 C18 DE6 sing 99 n n C03 C02 DE6 sing 100 n n C01 C02 DE6 doub 101 n y C01 C44 DE6 sing 102 n y C02 C42 DE6 sing 103 n y C18 N19 DE6 sing 104 n n C44 C43 DE6 doub 105 n y C42 C41 DE6 doub 106 n y O39 C38 DE6 doub 107 n n N19 C20 DE6 sing 108 n n C43 C41 DE6 sing 109 n y C41 C40 DE6 sing 110 n n O21 C20 DE6 doub 111 n n C20 C22 DE6 sing 112 n n C38 C40 DE6 sing 113 n n C38 N37 DE6 sing 114 n n O30 C29 DE6 doub 115 n n C29 C31 DE6 sing 116 n n C29 N28 DE6 sing 117 n n C31 N37 DE6 sing 118 n n C31 C32 DE6 sing 119 n n N28 C22 DE6 sing 120 n n C22 C23 DE6 sing 121 n n C32 C33 DE6 sing 122 n n C33 C34 DE6 sing 123 n n C23 C24 DE6 sing 124 n n C34 C35 DE6 sing 125 n n C24 C25 DE6 sing 126 n n C35 N36 DE6 sing 127 n n C25 C26 DE6 sing 128 n n C26 N27 DE6 sing 129 n n C10 H1 DE6 sing 130 n n C15 H2 DE6 sing 131 n n C15 H3 DE6 sing 132 n n C17 H4 DE6 sing 133 n n C17 H5 DE6 sing 134 n n C22 H6 DE6 sing 135 n n C24 H7 DE6 sing 136 n n C24 H8 DE6 sing 137 n n C26 H9 DE6 sing 138 n n C26 H10 DE6 sing 139 n n C01 H11 DE6 sing 140 n n C03 H12 DE6 sing 141 n n C03 H13 DE6 sing 142 n n C06 H14 DE6 sing 143 n n C07 H15 DE6 sing 144 n n C07 H16 DE6 sing 145 n n C07 H17 DE6 sing 146 n n C16 H18 DE6 sing 147 n n C16 H19 DE6 sing 148 n n C18 H20 DE6 sing 149 n n C18 H21 DE6 sing 150 n n C23 H22 DE6 sing 151 n n C23 H23 DE6 sing 152 n n C25 H24 DE6 sing 153 n n C25 H25 DE6 sing 154 n n C31 H26 DE6 sing 155 n n C32 H27 DE6 sing 156 n n C32 H28 DE6 sing 157 n n C33 H29 DE6 sing 158 n n C33 H30 DE6 sing 159 n n C34 H31 DE6 sing 160 n n C34 H32 DE6 sing 161 n n C35 H33 DE6 sing 162 n n C35 H34 DE6 sing 163 n n C40 H35 DE6 sing 164 n n C40 H36 DE6 sing 165 n n C42 H37 DE6 sing 166 n n C43 H38 DE6 sing 167 n n C44 H39 DE6 sing 168 n n N04 H40 DE6 sing 169 n n N08 H41 DE6 sing 170 n n N11 H42 DE6 sing 171 n n N13 H43 DE6 sing 172 n n N13 H44 DE6 sing 173 n n N14 H45 DE6 sing 174 n n N19 H46 DE6 sing 175 n n N27 H47 DE6 sing 176 n n N27 H48 DE6 sing 177 n n N28 H50 DE6 sing 178 n n N36 H51 DE6 sing 179 n n N36 H52 DE6 sing 180 n n N37 H54 DE6 sing 181 n n # _atom_sites.entry_id 6KK5 _atom_sites.fract_transf_matrix[1][1] 0.023514 _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] 0.023514 _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] 0.004643 _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 3 DE6 B 1 201 201 DE6 LIG . D 4 HOH A 1 101 50 HOH HOH . D 4 HOH A 2 102 10 HOH HOH . D 4 HOH A 3 103 31 HOH HOH . D 4 HOH A 4 104 26 HOH HOH . D 4 HOH A 5 105 29 HOH HOH . D 4 HOH A 6 106 32 HOH HOH . D 4 HOH A 7 107 8 HOH HOH . D 4 HOH A 8 108 17 HOH HOH . D 4 HOH A 9 109 40 HOH HOH . D 4 HOH A 10 110 30 HOH HOH . D 4 HOH A 11 111 45 HOH HOH . D 4 HOH A 12 112 51 HOH HOH . E 4 HOH B 1 301 6 HOH HOH . E 4 HOH B 2 302 37 HOH HOH . E 4 HOH B 3 303 15 HOH HOH . E 4 HOH B 4 304 18 HOH HOH . E 4 HOH B 5 305 21 HOH HOH . E 4 HOH B 6 306 19 HOH HOH . E 4 HOH B 7 307 5 HOH HOH . E 4 HOH B 8 308 16 HOH HOH . E 4 HOH B 9 309 13 HOH HOH . E 4 HOH B 10 310 23 HOH HOH . E 4 HOH B 11 311 2 HOH HOH . E 4 HOH B 12 312 34 HOH HOH . E 4 HOH B 13 313 9 HOH HOH . E 4 HOH B 14 314 20 HOH HOH . E 4 HOH B 15 315 3 HOH HOH . E 4 HOH B 16 316 1 HOH HOH . E 4 HOH B 17 317 7 HOH HOH . E 4 HOH B 18 318 22 HOH HOH . E 4 HOH B 19 319 14 HOH HOH . E 4 HOH B 20 320 42 HOH HOH . E 4 HOH B 21 321 12 HOH HOH . E 4 HOH B 22 322 33 HOH HOH . E 4 HOH B 23 323 46 HOH HOH . E 4 HOH B 24 324 36 HOH HOH . E 4 HOH B 25 325 24 HOH HOH . E 4 HOH B 26 326 11 HOH HOH . E 4 HOH B 27 327 27 HOH HOH . E 4 HOH B 28 328 28 HOH HOH . E 4 HOH B 29 329 41 HOH HOH . E 4 HOH B 30 330 43 HOH HOH . E 4 HOH B 31 331 49 HOH HOH . E 4 HOH B 32 332 47 HOH HOH . E 4 HOH B 33 333 4 HOH HOH . E 4 HOH B 34 334 39 HOH HOH . E 4 HOH B 35 335 38 HOH HOH . E 4 HOH B 36 336 44 HOH HOH . E 4 HOH B 37 337 35 HOH HOH . E 4 HOH B 38 338 48 HOH HOH . E 4 HOH B 39 339 25 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 C10 DE6 . . . C 3 -5.405 5.997 -18.725 1 47.28 ? C10 DE6 201 B 1 HETATM 2 C C15 DE6 . . . C 3 -6.833 5.544 -19.014 1 47.17 ? C15 DE6 201 B 1 HETATM 3 C C17 DE6 . . . C 3 -9.118 5.279 -18.141 1 37.31 ? C17 DE6 201 B 1 HETATM 4 C C20 DE6 . . . C 3 -8.925 5.777 -14.765 1 46.84 ? C20 DE6 201 B 1 HETATM 5 C C22 DE6 . . . C 3 -8.407 5.1 -13.503 1 45.04 ? C22 DE6 201 B 1 HETATM 6 C C24 DE6 . . . C 3 -8.035 5.26 -11.092 1 38.96 ? C24 DE6 201 B 1 HETATM 7 C C26 DE6 . . . C 3 -7.947 3.271 -9.651 1 46.42 ? C26 DE6 201 B 1 HETATM 8 C C01 DE6 . . . C 3 0.178 7.605 -17.188 1 62.67 ? C01 DE6 201 B 1 HETATM 9 C C02 DE6 . . . C 3 -0.959 8.4 -17.144 1 59.22 ? C02 DE6 201 B 1 HETATM 10 C C03 DE6 . . . C 3 -1.134 9.576 -18.103 1 57.46 ? C03 DE6 201 B 1 HETATM 11 C C05 DE6 . . . C 3 -3.551 10.101 -18.585 1 54.08 ? C05 DE6 201 B 1 HETATM 12 C C06 DE6 . . . C 3 -4.795 9.839 -19.43 1 51.34 ? C06 DE6 201 B 1 HETATM 13 C C07 DE6 . . . C 3 -6.049 10.537 -18.898 1 54.9 ? C07 DE6 201 B 1 HETATM 14 C C09 DE6 . . . C 3 -5.251 7.508 -18.466 1 53.97 ? C09 DE6 201 B 1 HETATM 15 C C12 DE6 . . . C 3 -3.162 5.418 -19.727 1 45.71 ? C12 DE6 201 B 1 HETATM 16 C C16 DE6 . . . C 3 -7.766 5.939 -17.872 1 35.65 ? C16 DE6 201 B 1 HETATM 17 C C18 DE6 . . . C 3 -10.068 5.612 -16.99 1 42.7 ? C18 DE6 201 B 1 HETATM 18 C C23 DE6 . . . C 3 -8.79 5.883 -12.256 1 43.25 ? C23 DE6 201 B 1 HETATM 19 C C25 DE6 . . . C 3 -8.898 4.2 -10.409 1 40.52 ? C25 DE6 201 B 1 HETATM 20 C C29 DE6 . . . C 3 -6.413 3.627 -13.84 1 41.61 ? C29 DE6 201 B 1 HETATM 21 C C31 DE6 . . . C 3 -4.899 3.421 -13.828 1 47.07 ? C31 DE6 201 B 1 HETATM 22 C C32 DE6 . . . C 3 -4.603 2.558 -12.598 1 44.71 ? C32 DE6 201 B 1 HETATM 23 C C33 DE6 . . . C 3 -3.113 2.297 -12.458 1 48.36 ? C33 DE6 201 B 1 HETATM 24 C C34 DE6 . . . C 3 -2.927 1.483 -11.178 1 48.84 ? C34 DE6 201 B 1 HETATM 25 C C35 DE6 . . . C 3 -1.476 1.005 -11.061 1 52.99 ? C35 DE6 201 B 1 HETATM 26 C C38 DE6 . . . C 3 -3.616 5.473 -14.697 1 57.7 ? C38 DE6 201 B 1 HETATM 27 C C40 DE6 . . . C 3 -2.922 6.789 -14.335 1 59.63 ? C40 DE6 201 B 1 HETATM 28 C C41 DE6 . . . C 3 -1.808 7.065 -15.343 1 57.72 ? C41 DE6 201 B 1 HETATM 29 C C42 DE6 . . . C 3 -1.952 8.124 -16.223 1 59.4 ? C42 DE6 201 B 1 HETATM 30 C C43 DE6 . . . C 3 -0.673 6.271 -15.386 1 48.84 ? C43 DE6 201 B 1 HETATM 31 C C44 DE6 . . . C 3 0.325 6.543 -16.307 1 56.84 ? C44 DE6 201 B 1 HETATM 32 N N04 DE6 . . . C 3 -2.339 9.365 -18.888 1 56.19 ? N04 DE6 201 B 1 HETATM 33 N N08 DE6 . . . C 3 -4.97 8.399 -19.586 1 50.76 ? N08 DE6 201 B 1 HETATM 34 N N11 DE6 . . . C 3 -4.591 5.566 -19.847 1 46.75 ? N11 DE6 201 B 1 HETATM 35 N N13 DE6 . . . C 3 -2.584 5.658 -18.638 1 47.94 ? N13 DE6 201 B 1 HETATM 36 N N14 DE6 . . . C 3 -2.406 4.985 -20.881 1 52.74 ? N14 DE6 201 B 1 HETATM 37 N N19 DE6 . . . C 3 -9.57 4.982 -15.78 1 44.53 ? N19 DE6 201 B 1 HETATM 38 N N27 DE6 . . . C 3 -8.638 2.523 -8.628 1 41.89 ? N27 DE6 201 B 1 HETATM 39 N N28 DE6 . . . C 3 -6.972 4.927 -13.522 1 40.61 ? N28 DE6 201 B 1 HETATM 40 N N36 DE6 . . . C 3 -1.171 0.756 -9.657 1 53.86 ? N36 DE6 201 B 1 HETATM 41 N N37 DE6 . . . C 3 -4.221 4.694 -13.62 1 49.75 ? N37 DE6 201 B 1 HETATM 42 O O21 DE6 . . . C 3 -8.817 6.948 -14.903 1 52.04 ? O21 DE6 201 B 1 HETATM 43 O O30 DE6 . . . C 3 -7.124 2.709 -14.069 1 38.67 ? O30 DE6 201 B 1 HETATM 44 O O39 DE6 . . . C 3 -3.649 5.107 -15.826 1 51.73 ? O39 DE6 201 B 1 HETATM 45 O O45 DE6 . . . C 3 -5.341 7.962 -17.364 1 49.22 ? O45 DE6 201 B 1 HETATM 46 O O46 DE6 . . . C 3 -3.573 10.883 -17.692 1 52.59 ? O46 DE6 201 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #