data_1G2M # _model_server_result.job_id S1-ZWQuKQhF3XMF7_DGejw _model_server_result.datetime_utc '2024-11-22 02:26:00' _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 1g2m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 1G2M # _exptl.entry_id 1G2M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 423.513 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1-YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}-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 90 _cell.entry_id 1G2M _cell.length_a 57.4 _cell.length_b 73.2 _cell.length_c 79.7 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G2M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 7 A CYS 22 1_555 A SG CYS 12 A CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 27 A CYS 42 1_555 A SG CYS 43 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 A SG CYS 108 A CYS 122 1_555 B SG CYS 87 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 156 A CYS 168 1_555 A SG CYS 170 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 181 A CYS 191 1_555 A SG CYS 209 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 44 B CYS 389 1_555 B SG CYS 55 B CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 51 B CYS 396 1_555 B SG CYS 64 B CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 66 B CYS 411 1_555 B SG CYS 79 B CYS 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc1 A OD1 ASP 56 A ASP 70 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc2 A O ASN 58 A ASN 72 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc3 A O GLN 61 A GLN 75 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc4 A OE1 GLU 63 A GLU 77 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.355 ? metalc ? metalc5 A OE1 GLU 66 A GLU 80 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc6 A OE2 GLU 66 A GLU 80 1_555 C CA CA . A CA 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? # _chem_comp.formula 'C25 H25 N7' _chem_comp.formula_weight 423.513 _chem_comp.id R11 _chem_comp.mon_nstd_flag . _chem_comp.name 4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1-YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}-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 N1 C1 R11 doub 275 z n N1 HN1 R11 sing 276 n n N2 C1 R11 sing 277 n n N2 HN21 R11 sing 278 n n N2 HN22 R11 sing 279 n n C1 C2 R11 sing 280 n n C2 C3 R11 doub 281 n y C2 C7 R11 sing 282 n y C3 C4 R11 sing 283 n y C3 HC3 R11 sing 284 n n C4 C5 R11 doub 285 n y C4 HC4 R11 sing 286 n n C5 C6 R11 sing 287 n y C5 N R11 sing 288 n n C6 C7 R11 doub 289 n y C6 HC6 R11 sing 290 n n C7 HC7 R11 sing 291 n n N C R11 sing 292 n n N HN R11 sing 293 n n C C8 R11 sing 294 n n C H1C R11 sing 295 n n C H2C R11 sing 296 n n N3 C8 R11 doub 297 n y N3 C7A R11 sing 298 n y C8 N9 R11 sing 299 n y N9 C3A R11 sing 300 n y N9 C14 R11 sing 301 n n C3A C7A R11 doub 302 n y C3A C10 R11 sing 303 n y C7A C13 R11 sing 304 n y C10 C11 R11 doub 305 n y C10 H10C R11 sing 306 n n C11 C12 R11 sing 307 n y C11 H11C R11 sing 308 n n C12 C13 R11 doub 309 n y C12 C9 R11 sing 310 n n C13 H13C R11 sing 311 n n C14 H141 R11 sing 312 n n C14 H142 R11 sing 313 n n C14 H143 R11 sing 314 n n C9 N4 R11 sing 315 n n C9 HC91 R11 sing 316 n n C9 HC92 R11 sing 317 n n N4 C15 R11 sing 318 n y N4 C18 R11 sing 319 n y C15 N16 R11 doub 320 n y C15 C23 R11 sing 321 n n N16 C17 R11 sing 322 n y C17 C18 R11 doub 323 n y C17 C19 R11 sing 324 n y C18 C22 R11 sing 325 n y C19 C20 R11 doub 326 n y C19 H19C R11 sing 327 n n C20 C21 R11 sing 328 n y C20 H20C R11 sing 329 n n C21 C22 R11 doub 330 n y C21 H21C R11 sing 331 n n C22 H22C R11 sing 332 n n C23 H231 R11 sing 333 n n C23 H232 R11 sing 334 n n C23 H233 R11 sing 335 n n # _atom_sites.entry_id 1G2M _atom_sites.fract_transf_matrix[1][1] 0.017422 _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] 0.013661 _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] 0.012547 _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 CA A 1 999 999 CA CA . D 4 R11 A 1 1 1 R11 R11 . # 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 N N1 R11 . . . D 4 9.7 6.798 28.768 1 13.73 ? N1 R11 1 A 1 HETATM 2 N N2 R11 . . . D 4 11.808 7.025 28.325 1 21.81 ? N2 R11 1 A 1 HETATM 3 C C1 R11 . . . D 4 10.582 7.301 27.935 1 14.24 ? C1 R11 1 A 1 HETATM 4 C C2 R11 . . . D 4 10.251 7.984 26.762 1 10.8 ? C2 R11 1 A 1 HETATM 5 C C3 R11 . . . D 4 8.964 7.823 26.149 1 15.02 ? C3 R11 1 A 1 HETATM 6 C C4 R11 . . . D 4 8.624 8.505 24.97 1 20.88 ? C4 R11 1 A 1 HETATM 7 C C5 R11 . . . D 4 9.548 9.374 24.35 1 21.71 ? C5 R11 1 A 1 HETATM 8 C C6 R11 . . . D 4 10.824 9.561 24.919 1 16.74 ? C6 R11 1 A 1 HETATM 9 C C7 R11 . . . D 4 11.176 8.878 26.108 1 11.78 ? C7 R11 1 A 1 HETATM 10 N N R11 . . . D 4 9.219 10.08 23.141 1 27.69 ? N R11 1 A 1 HETATM 11 C C R11 . . . D 4 8.096 9.808 22.217 1 30.5 ? C R11 1 A 1 HETATM 12 N N3 R11 . . . D 4 7.315 7.409 22.008 1 38.31 ? N3 R11 1 A 1 HETATM 13 C C8 R11 . . . D 4 8.112 8.443 21.504 1 34.24 ? C8 R11 1 A 1 HETATM 14 N N9 R11 . . . D 4 8.909 8.231 20.366 1 34.73 ? N9 R11 1 A 1 HETATM 15 C C3A R11 . . . D 4 8.571 6.907 20.123 1 35.73 ? C3A R11 1 A 1 HETATM 16 C C7A R11 . . . D 4 7.624 6.422 21.101 1 36.91 ? C7A R11 1 A 1 HETATM 17 C C10 R11 . . . D 4 9.034 6.038 19.083 1 36.61 ? C10 R11 1 A 1 HETATM 18 C C11 R11 . . . D 4 8.551 4.725 19.027 1 38.77 ? C11 R11 1 A 1 HETATM 19 C C12 R11 . . . D 4 7.617 4.235 19.984 1 43.12 ? C12 R11 1 A 1 HETATM 20 C C13 R11 . . . D 4 7.145 5.077 21.03 1 40.2 ? C13 R11 1 A 1 HETATM 21 C C14 R11 . . . D 4 9.834 9.141 19.634 1 40.04 ? C14 R11 1 A 1 HETATM 22 C C9 R11 . . . D 4 7.121 2.782 19.862 1 46.64 ? C9 R11 1 A 1 HETATM 23 N N4 R11 . . . D 4 7.416 2.143 18.528 1 47.7 ? N4 R11 1 A 1 HETATM 24 C C15 R11 . . . D 4 6.635 1.976 17.36 1 49.47 ? C15 R11 1 A 1 HETATM 25 N N16 R11 . . . D 4 7.138 1.34 16.226 1 52.02 ? N16 R11 1 A 1 HETATM 26 C C17 R11 . . . D 4 8.402 1.054 16.701 1 48.38 ? C17 R11 1 A 1 HETATM 27 C C18 R11 . . . D 4 8.573 1.522 18.061 1 45.57 ? C18 R11 1 A 1 HETATM 28 C C19 R11 . . . D 4 9.475 0.387 16.026 1 47.62 ? C19 R11 1 A 1 HETATM 29 C C20 R11 . . . D 4 10.698 0.2 16.706 1 46 ? C20 R11 1 A 1 HETATM 30 C C21 R11 . . . D 4 10.873 0.656 18.035 1 48.61 ? C21 R11 1 A 1 HETATM 31 C C22 R11 . . . D 4 9.832 1.318 18.723 1 44.92 ? C22 R11 1 A 1 HETATM 32 C C23 R11 . . . D 4 5.204 2.489 17.288 1 51.53 ? C23 R11 1 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #