data_1RTF # _model_server_result.job_id -Od1LRjKDSw3FjNQOju6Hg _model_server_result.datetime_utc '2024-12-08 11:57:22' _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 1rtf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":245}' # _entry.id 1RTF # _exptl.entry_id 1RTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BENZAMIDINE _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 120 _cell.entry_id 1RTF _cell.length_a 59.2 _cell.length_b 59.2 _cell.length_c 136.33 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 6 A CYS 1 1_555 B SG CYS 120 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 32 B CYS 42 1_555 B SG CYS 48 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf3 B SG CYS 40 B CYS 50 1_555 B SG CYS 109 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 134 B CYS 136 1_555 B SG CYS 209 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 B SG CYS 166 B CYS 168 1_555 B SG CYS 182 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 199 B CYS 191 1_555 B SG CYS 227 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C7 H8 N2' _chem_comp.formula_weight 120.152 _chem_comp.id BEN _chem_comp.mon_nstd_flag . _chem_comp.name BENZAMIDINE _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 C1 C2 BEN doub 70 n y C1 C6 BEN sing 71 n y C1 C BEN sing 72 n n C2 C3 BEN sing 73 n y C2 H2 BEN sing 74 n n C3 C4 BEN doub 75 n y C3 H3 BEN sing 76 n n C4 C5 BEN sing 77 n y C4 H4 BEN sing 78 n n C5 C6 BEN doub 79 n y C5 H5 BEN sing 80 n n C6 H6 BEN sing 81 n n C N1 BEN doub 82 e n C N2 BEN sing 83 n n N1 HN1 BEN sing 84 n n N2 HN21 BEN sing 85 n n N2 HN22 BEN sing 86 n n # _atom_sites.entry_id 1RTF _atom_sites.fract_transf_matrix[1][1] 0.016892 _atom_sites.fract_transf_matrix[1][2] 0.009753 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019505 _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] 0.007335 _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 PO4 B 1 1 1 PO4 PO4 . D 4 BEN B 1 245 1 BEN BEN . E 5 HOH A 1 13 2 HOH HOH . E 5 HOH A 2 14 33 HOH HOH . E 5 HOH A 3 15 34 HOH HOH . E 5 HOH A 4 16 46 HOH HOH . F 5 HOH B 1 246 1 HOH HOH . F 5 HOH B 2 247 3 HOH HOH . F 5 HOH B 3 248 4 HOH HOH . F 5 HOH B 4 249 5 HOH HOH . F 5 HOH B 5 250 6 HOH HOH . F 5 HOH B 6 251 7 HOH HOH . F 5 HOH B 7 252 8 HOH HOH . F 5 HOH B 8 253 9 HOH HOH . F 5 HOH B 9 254 10 HOH HOH . F 5 HOH B 10 255 11 HOH HOH . F 5 HOH B 11 256 12 HOH HOH . F 5 HOH B 12 257 13 HOH HOH . F 5 HOH B 13 258 14 HOH HOH . F 5 HOH B 14 259 15 HOH HOH . F 5 HOH B 15 260 16 HOH HOH . F 5 HOH B 16 261 17 HOH HOH . F 5 HOH B 17 262 18 HOH HOH . F 5 HOH B 18 263 19 HOH HOH . F 5 HOH B 19 264 20 HOH HOH . F 5 HOH B 20 265 21 HOH HOH . F 5 HOH B 21 266 22 HOH HOH . F 5 HOH B 22 267 23 HOH HOH . F 5 HOH B 23 268 24 HOH HOH . F 5 HOH B 24 269 25 HOH HOH . F 5 HOH B 25 270 26 HOH HOH . F 5 HOH B 26 271 27 HOH HOH . F 5 HOH B 27 272 28 HOH HOH . F 5 HOH B 28 273 29 HOH HOH . F 5 HOH B 29 274 30 HOH HOH . F 5 HOH B 30 275 31 HOH HOH . F 5 HOH B 31 276 32 HOH HOH . F 5 HOH B 32 277 35 HOH HOH . F 5 HOH B 33 278 36 HOH HOH . F 5 HOH B 34 279 37 HOH HOH . F 5 HOH B 35 280 38 HOH HOH . F 5 HOH B 36 281 39 HOH HOH . F 5 HOH B 37 282 40 HOH HOH . F 5 HOH B 38 283 41 HOH HOH . F 5 HOH B 39 284 42 HOH HOH . F 5 HOH B 40 285 43 HOH HOH . F 5 HOH B 41 286 44 HOH HOH . F 5 HOH B 42 287 45 HOH HOH . F 5 HOH B 43 288 47 HOH HOH . F 5 HOH B 44 289 48 HOH HOH . F 5 HOH B 45 290 49 HOH HOH . F 5 HOH B 46 291 50 HOH HOH . F 5 HOH B 47 292 51 HOH HOH . F 5 HOH B 48 293 52 HOH HOH . F 5 HOH B 49 294 53 HOH HOH . F 5 HOH B 50 295 54 HOH HOH . F 5 HOH B 51 296 55 HOH HOH . F 5 HOH B 52 297 56 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 C1 BEN . . . D 4 -6.921 31.206 33.893 1 23.35 ? C1 BEN 245 B 1 HETATM 2 C C2 BEN . . . D 4 -8.189 30.836 34.344 1 23.15 ? C2 BEN 245 B 1 HETATM 3 C C3 BEN . . . D 4 -8.335 29.863 35.342 1 20.74 ? C3 BEN 245 B 1 HETATM 4 C C4 BEN . . . D 4 -7.206 29.254 35.893 1 19.45 ? C4 BEN 245 B 1 HETATM 5 C C5 BEN . . . D 4 -5.932 29.618 35.445 1 20.83 ? C5 BEN 245 B 1 HETATM 6 C C6 BEN . . . D 4 -5.794 30.589 34.45 1 20.99 ? C6 BEN 245 B 1 HETATM 7 C C BEN . . . D 4 -6.767 32.249 32.859 1 24.3 ? C BEN 245 B 1 HETATM 8 N N1 BEN . . . D 4 -5.57 32.641 32.497 1 24.56 ? N1 BEN 245 B 1 HETATM 9 N N2 BEN . . . D 4 -7.824 32.785 32.299 1 24.58 ? N2 BEN 245 B 1 HETATM 10 H HN1 BEN . . . D 4 -4.758 32.237 32.919 1 0 ? HN1 BEN 245 B 1 HETATM 11 H HN21 BEN . . . D 4 -8.735 32.481 32.572 1 0 ? HN21 BEN 245 B 1 HETATM 12 H HN22 BEN . . . D 4 -7.718 33.49 31.599 1 0 ? HN22 BEN 245 B 1 HETATM 13 H HN12 BEN . . . D 4 -5.47 33.348 31.797 1 0 ? HN12 BEN 245 B 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #