data_6GOB # _model_server_result.job_id kk2cX_VxNUbXMe9SBmfQOA _model_server_result.datetime_utc '2024-10-18 12:27:06' _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 6gob # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":207}' # _entry.id 6GOB # _exptl.entry_id 6GOB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.689 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N,N-pyridylbenzimidazole derivative-Pd complex' _entity.pdbx_number_of_molecules 5 _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 6GOB _cell.length_a 79.487 _cell.length_b 79.487 _cell.length_c 37.309 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GOB _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N 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 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A ND1 HIS 15 A HIS 15 1_555 J PD F6Q . A F6Q 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc2 A OD1 ASN 77 A ASN 77 1_555 C PD PD . A PD 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc3 A OD2 ASP 87 A ASP 87 1_555 B PD PD . A PD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 A OD1 ASP 101 A ASP 101 1_555 H PD F6Q . A F6Q 207 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc5 A OD1 ASP 101 A ASP 101 1_555 H PD F6Q . A F6Q 207 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc6 B PD PD . A PD 201 1_555 O O HOH . A HOH 373 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc7 B PD PD . A PD 201 1_555 O O HOH . A HOH 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc8 C PD PD . A PD 202 1_555 O O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc9 I PD F6Q . A F6Q 208 1_555 O O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc10 I PD F6Q . A F6Q 208 1_555 O O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? # _chem_comp.formula 'C15 H15 Cl2 N3 O3 Pd S 2' _chem_comp.formula_weight 494.689 _chem_comp.id F6Q _chem_comp.mon_nstd_flag . _chem_comp.name 'N,N-pyridylbenzimidazole derivative-Pd complex' _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 OAU SAV F6Q doub 83 n n SAV OAS F6Q doub 84 n n SAV OAT F6Q sing 85 n n SAV CAP F6Q sing 86 n n CAP CAO F6Q sing 87 n n CAO CAN F6Q sing 88 n n CAN NAM F6Q sing 89 n n NAM CAB F6Q sing 90 n y NAM CAG F6Q sing 91 n y CAB CAC F6Q doub 92 n y CAB CAA F6Q sing 93 n y CAC CAD F6Q sing 94 n y CAD CAE F6Q doub 95 n y CAE CAF F6Q sing 96 n y CAF CAA F6Q doub 97 n y CAA NAL F6Q sing 98 n y NAL CAG F6Q doub 99 n y NAL PD F6Q sing 100 n n CAG CAH F6Q sing 101 n n CAH NAQ F6Q doub 102 n y CAH CAR F6Q sing 103 n y NAQ CAI F6Q sing 104 n y NAQ PD F6Q sing 105 n n CAI CAK F6Q doub 106 n y CAK CAJ F6Q sing 107 n y CAJ CAR F6Q doub 108 n y CL2 PD F6Q sing 109 n n CAP H1 F6Q sing 110 n n CAP H2 F6Q sing 111 n n CAO H3 F6Q sing 112 n n CAO H4 F6Q sing 113 n n CAN H5 F6Q sing 114 n n CAN H6 F6Q sing 115 n n CAC H7 F6Q sing 116 n n CAD H8 F6Q sing 117 n n CAE H9 F6Q sing 118 n n CAF H10 F6Q sing 119 n n CAI H11 F6Q sing 120 n n CAK H12 F6Q sing 121 n n CAJ H13 F6Q sing 122 n n CAR H14 F6Q sing 123 n n PD CL1 F6Q sing 124 n n OAT H16 F6Q sing 125 n n # _atom_sites.entry_id 6GOB _atom_sites.fract_transf_matrix[1][1] 0.012581 _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] 0.012581 _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] 0.026803 _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 B 2 PD A 1 201 5 PD PD . C 2 PD A 1 202 6 PD PD . D 3 NO3 A 1 203 1 NO3 NO3 . E 3 NO3 A 1 204 2 NO3 NO3 . F 4 F6Q A 1 205 1 F6Q XXX . G 4 F6Q A 1 206 2 F6Q XXX . H 4 F6Q A 1 207 3 F6Q XXX . I 4 F6Q A 1 208 4 F6Q XXX . J 4 F6Q A 1 209 5 F6Q XXX . K 5 SO4 A 1 210 1 SO4 SO4 . L 5 SO4 A 1 211 2 SO4 SO4 . M 6 CL A 1 212 7 CL CL . N 6 CL A 1 213 8 CL CL . O 7 HOH A 1 301 125 HOH HOH . O 7 HOH A 2 302 133 HOH HOH . O 7 HOH A 3 303 94 HOH HOH . O 7 HOH A 4 304 64 HOH HOH . O 7 HOH A 5 305 7 HOH HOH . O 7 HOH A 6 306 128 HOH HOH . O 7 HOH A 7 307 37 HOH HOH . O 7 HOH A 8 308 91 HOH HOH . O 7 HOH A 9 309 167 HOH HOH . O 7 HOH A 10 310 24 HOH HOH . O 7 HOH A 11 311 137 HOH HOH . O 7 HOH A 12 312 86 HOH HOH . O 7 HOH A 13 313 144 HOH HOH . O 7 HOH A 14 314 36 HOH HOH . O 7 HOH A 15 315 102 HOH HOH . O 7 HOH A 16 316 93 HOH HOH . O 7 HOH A 17 317 3 HOH HOH . O 7 HOH A 18 318 153 HOH HOH . O 7 HOH A 19 319 19 HOH HOH . O 7 HOH A 20 320 5 HOH HOH . O 7 HOH A 21 321 68 HOH HOH . O 7 HOH A 22 322 140 HOH HOH . O 7 HOH A 23 323 83 HOH HOH . O 7 HOH A 24 324 4 HOH HOH . O 7 HOH A 25 325 1 HOH HOH . O 7 HOH A 26 326 129 HOH HOH . O 7 HOH A 27 327 77 HOH HOH . O 7 HOH A 28 328 56 HOH HOH . O 7 HOH A 29 329 52 HOH HOH . O 7 HOH A 30 330 89 HOH HOH . O 7 HOH A 31 331 48 HOH HOH . O 7 HOH A 32 332 163 HOH HOH . O 7 HOH A 33 333 32 HOH HOH . O 7 HOH A 34 334 39 HOH HOH . O 7 HOH A 35 335 164 HOH HOH . O 7 HOH A 36 336 50 HOH HOH . O 7 HOH A 37 337 34 HOH HOH . O 7 HOH A 38 338 151 HOH HOH . O 7 HOH A 39 339 95 HOH HOH . O 7 HOH A 40 340 43 HOH HOH . O 7 HOH A 41 341 59 HOH HOH . O 7 HOH A 42 342 8 HOH HOH . O 7 HOH A 43 343 98 HOH HOH . O 7 HOH A 44 344 105 HOH HOH . O 7 HOH A 45 345 72 HOH HOH . O 7 HOH A 46 346 101 HOH HOH . O 7 HOH A 47 347 135 HOH HOH . O 7 HOH A 48 348 134 HOH HOH . O 7 HOH A 49 349 16 HOH HOH . O 7 HOH A 50 350 26 HOH HOH . O 7 HOH A 51 351 162 HOH HOH . O 7 HOH A 52 352 38 HOH HOH . O 7 HOH A 53 353 35 HOH HOH . O 7 HOH A 54 354 22 HOH HOH . O 7 HOH A 55 355 113 HOH HOH . O 7 HOH A 56 356 20 HOH HOH . O 7 HOH A 57 357 6 HOH HOH . O 7 HOH A 58 358 138 HOH HOH . O 7 HOH A 59 359 146 HOH HOH . O 7 HOH A 60 360 71 HOH HOH . O 7 HOH A 61 361 108 HOH HOH . O 7 HOH A 62 362 157 HOH HOH . O 7 HOH A 63 363 2 HOH HOH . O 7 HOH A 64 364 47 HOH HOH . O 7 HOH A 65 365 88 HOH HOH . O 7 HOH A 66 366 63 HOH HOH . O 7 HOH A 67 367 126 HOH HOH . O 7 HOH A 68 368 29 HOH HOH . O 7 HOH A 69 369 15 HOH HOH . O 7 HOH A 70 370 165 HOH HOH . O 7 HOH A 71 371 73 HOH HOH . O 7 HOH A 72 372 53 HOH HOH . O 7 HOH A 73 373 121 HOH HOH . O 7 HOH A 74 374 21 HOH HOH . O 7 HOH A 75 375 118 HOH HOH . O 7 HOH A 76 376 9 HOH HOH . O 7 HOH A 77 377 116 HOH HOH . O 7 HOH A 78 378 27 HOH HOH . O 7 HOH A 79 379 44 HOH HOH . O 7 HOH A 80 380 57 HOH HOH . O 7 HOH A 81 381 152 HOH HOH . O 7 HOH A 82 382 143 HOH HOH . O 7 HOH A 83 383 147 HOH HOH . O 7 HOH A 84 384 141 HOH HOH . O 7 HOH A 85 385 75 HOH HOH . O 7 HOH A 86 386 107 HOH HOH . O 7 HOH A 87 387 110 HOH HOH . O 7 HOH A 88 388 12 HOH HOH . O 7 HOH A 89 389 18 HOH HOH . O 7 HOH A 90 390 60 HOH HOH . O 7 HOH A 91 391 122 HOH HOH . O 7 HOH A 92 392 123 HOH HOH . O 7 HOH A 93 393 120 HOH HOH . O 7 HOH A 94 394 66 HOH HOH . O 7 HOH A 95 395 65 HOH HOH . O 7 HOH A 96 396 90 HOH HOH . O 7 HOH A 97 397 67 HOH HOH . O 7 HOH A 98 398 13 HOH HOH . O 7 HOH A 99 399 103 HOH HOH . O 7 HOH A 100 400 132 HOH HOH . O 7 HOH A 101 401 80 HOH HOH . O 7 HOH A 102 402 100 HOH HOH . O 7 HOH A 103 403 28 HOH HOH . O 7 HOH A 104 404 127 HOH HOH . O 7 HOH A 105 405 150 HOH HOH . O 7 HOH A 106 406 119 HOH HOH . O 7 HOH A 107 407 109 HOH HOH . O 7 HOH A 108 408 131 HOH HOH . O 7 HOH A 109 409 76 HOH HOH . O 7 HOH A 110 410 79 HOH HOH . O 7 HOH A 111 411 69 HOH HOH . O 7 HOH A 112 412 145 HOH HOH . O 7 HOH A 113 413 149 HOH HOH . O 7 HOH A 114 414 117 HOH HOH . O 7 HOH A 115 415 166 HOH HOH . O 7 HOH A 116 416 45 HOH HOH . O 7 HOH A 117 417 46 HOH HOH . O 7 HOH A 118 418 130 HOH HOH . O 7 HOH A 119 419 70 HOH HOH . O 7 HOH A 120 420 82 HOH HOH . O 7 HOH A 121 421 92 HOH HOH . O 7 HOH A 122 422 17 HOH HOH . O 7 HOH A 123 423 58 HOH HOH . O 7 HOH A 124 424 148 HOH HOH . O 7 HOH A 125 425 87 HOH HOH . O 7 HOH A 126 426 42 HOH HOH . O 7 HOH A 127 427 96 HOH HOH . O 7 HOH A 128 428 156 HOH HOH . O 7 HOH A 129 429 106 HOH HOH . O 7 HOH A 130 430 111 HOH HOH . O 7 HOH A 131 431 154 HOH HOH . O 7 HOH A 132 432 54 HOH HOH . O 7 HOH A 133 433 40 HOH HOH . O 7 HOH A 134 434 136 HOH HOH . O 7 HOH A 135 435 25 HOH HOH . O 7 HOH A 136 436 155 HOH HOH . O 7 HOH A 137 437 51 HOH HOH . O 7 HOH A 138 438 81 HOH HOH . O 7 HOH A 139 439 142 HOH HOH . O 7 HOH A 140 440 139 HOH HOH . O 7 HOH A 141 441 114 HOH HOH . O 7 HOH A 142 442 84 HOH HOH . O 7 HOH A 143 443 99 HOH HOH . O 7 HOH A 144 444 104 HOH HOH . O 7 HOH A 145 445 97 HOH HOH . O 7 HOH A 146 446 49 HOH HOH . O 7 HOH A 147 447 78 HOH HOH . O 7 HOH A 148 448 159 HOH HOH . O 7 HOH A 149 449 160 HOH HOH . O 7 HOH A 150 450 161 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 O OAU F6Q . . . H 4 -22.356 6.617 11.912 0.6 38.67 ? OAU F6Q 207 A 1 HETATM 2 S SAV F6Q . . . H 4 -22.994 5.343 11.336 0.6 40.34 ? SAV F6Q 207 A 1 HETATM 3 O OAS F6Q . . . H 4 -23.506 4.528 12.546 0.6 44.04 ? OAS F6Q 207 A 1 HETATM 4 O OAT F6Q . . . H 4 -21.945 4.561 10.55 0.6 40.89 ? OAT F6Q 207 A 1 HETATM 5 C CAP F6Q . . . H 4 -24.464 5.635 10.39 0.6 38.99 ? CAP F6Q 207 A 1 HETATM 6 C CAO F6Q . . . H 4 -25.393 4.398 10.279 0.6 35.22 ? CAO F6Q 207 A 1 HETATM 7 C CAN F6Q . . . H 4 -24.693 3.077 10.35 0.6 32.96 ? CAN F6Q 207 A 1 HETATM 8 N NAM F6Q . . . H 4 -25.164 2.243 9.176 0.6 30.5 ? NAM F6Q 207 A 1 HETATM 9 C CAB F6Q . . . H 4 -24.407 2.273 8.055 0.6 25.78 ? CAB F6Q 207 A 1 HETATM 10 C CAC F6Q . . . H 4 -23.398 3.072 7.693 0.6 26.01 ? CAC F6Q 207 A 1 HETATM 11 C CAD F6Q . . . H 4 -22.79 2.919 6.452 0.6 25.92 ? CAD F6Q 207 A 1 HETATM 12 C CAE F6Q . . . H 4 -23.217 1.921 5.599 0.6 24.07 ? CAE F6Q 207 A 1 HETATM 13 C CAF F6Q . . . H 4 -24.165 1.043 6.076 0.6 24.82 ? CAF F6Q 207 A 1 HETATM 14 C CAA F6Q . . . H 4 -24.765 1.266 7.254 0.6 26.22 ? CAA F6Q 207 A 1 HETATM 15 N NAL F6Q . . . H 4 -25.684 0.579 7.928 0.6 27.92 ? NAL F6Q 207 A 1 HETATM 16 C CAG F6Q . . . H 4 -25.959 1.18 9.109 0.6 25 ? CAG F6Q 207 A 1 HETATM 17 C CAH F6Q . . . H 4 -26.913 0.752 9.959 0.6 24.02 ? CAH F6Q 207 A 1 HETATM 18 N NAQ F6Q . . . H 4 -27.608 -0.343 9.573 0.6 22.6 ? NAQ F6Q 207 A 1 HETATM 19 C CAI F6Q . . . H 4 -28.615 -0.907 10.37 0.6 22.89 ? CAI F6Q 207 A 1 HETATM 20 C CAK F6Q . . . H 4 -28.944 -0.334 11.598 0.6 22.44 ? CAK F6Q 207 A 1 HETATM 21 C CAJ F6Q . . . H 4 -28.225 0.779 12.033 0.6 22.78 ? CAJ F6Q 207 A 1 HETATM 22 C CAR F6Q . . . H 4 -27.245 1.331 11.211 0.6 22.75 ? CAR F6Q 207 A 1 HETATM 23 CL CL2 F6Q . . . H 4 -27.867 -2.108 7.185 0.6 21.2 ? CL2 F6Q 207 A 1 HETATM 24 PD PD F6Q . . . H 4 -26.56 -0.713 7.16 0.6 26.72 ? PD F6Q 207 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #