data_6PL9 # _model_server_result.job_id GVwGaKVJ6u3thqFoQxY93A _model_server_result.datetime_utc '2025-01-01 18:50:01' _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 6pl9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 6PL9 # _exptl.entry_id 6PL9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 419.774 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-rhodapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole _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 6PL9 _cell.length_a 80.425 _cell.length_b 80.425 _cell.length_c 37.794 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PL9 _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 _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 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A NE2 HIS 15 A HIS 15 1_555 B RH ORS . A ORS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A O SER 60 A SER 60 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc3 A O CYS 64 A CYS 64 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 A OG SER 72 A SER 72 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc5 A O ARG 73 A ARG 73 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc6 A OD2 ASP 101 A ASP 101 1_555 C RH R1N . A R1N 202 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc7 D NA NA . A NA 203 1_555 E O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc8 D NA NA . A NA 203 1_555 E O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? # _chem_comp.formula 'C19 H25 Cl N2 Rh' _chem_comp.formula_weight 419.774 _chem_comp.id R1N _chem_comp.mon_nstd_flag . _chem_comp.name 2-(1-chloranyl-2,3,4,5,6-pentamethyl-1$l^{7}-rhodapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexan-1-yl)-1,3-dimethyl-benzimidazole _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 N1 R1N sing 309 n y C1 N2 R1N doub 310 n y C1 RH R1N sing 311 n n C2 N1 R1N sing 312 n n C3 N2 R1N sing 313 n n C4 C5 R1N doub 314 n y C4 C9 R1N sing 315 n y C4 N2 R1N sing 316 n y C5 C6 R1N sing 317 n y C5 N1 R1N sing 318 n y C6 C7 R1N doub 319 n y C7 C8 R1N sing 320 n y C8 C9 R1N doub 321 n y C10 C11 R1N sing 322 n n C10 C12 R1N sing 323 n n C10 C18 R1N sing 324 n n C10 RH R1N sing 325 n n C12 C13 R1N sing 326 n n C12 C14 R1N sing 327 n n C12 RH R1N sing 328 n n C14 C15 R1N sing 329 n n C14 C16 R1N sing 330 n n C14 RH R1N sing 331 n n C16 C17 R1N sing 332 n n C16 C18 R1N sing 333 n n C16 RH R1N sing 334 n n C18 C19 R1N sing 335 n n C18 RH R1N sing 336 n n RH CL1 R1N sing 337 n n C2 H1 R1N sing 338 n n C2 H2 R1N sing 339 n n C2 H3 R1N sing 340 n n C3 H4 R1N sing 341 n n C3 H5 R1N sing 342 n n C3 H6 R1N sing 343 n n C6 H7 R1N sing 344 n n C7 H8 R1N sing 345 n n C8 H9 R1N sing 346 n n C9 H10 R1N sing 347 n n C11 H11 R1N sing 348 n n C11 H12 R1N sing 349 n n C11 H13 R1N sing 350 n n C13 H14 R1N sing 351 n n C13 H15 R1N sing 352 n n C13 H16 R1N sing 353 n n C15 H17 R1N sing 354 n n C15 H18 R1N sing 355 n n C15 H19 R1N sing 356 n n C17 H20 R1N sing 357 n n C17 H21 R1N sing 358 n n C17 H22 R1N sing 359 n n C19 H23 R1N sing 360 n n C19 H24 R1N sing 361 n n C19 H25 R1N sing 362 n n # _atom_sites.entry_id 6PL9 _atom_sites.fract_transf_matrix[1][1] 0.012434 _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] 0.012434 _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] 0.026459 _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 ORS A 1 201 201 ORS R2N . C 3 R1N A 1 202 301 R1N R1N . D 4 NA A 1 203 1 NA NA . E 5 HOH A 1 301 52 HOH HOH . E 5 HOH A 2 302 13 HOH HOH . E 5 HOH A 3 303 103 HOH HOH . E 5 HOH A 4 304 105 HOH HOH . E 5 HOH A 5 305 131 HOH HOH . E 5 HOH A 6 306 70 HOH HOH . E 5 HOH A 7 307 10 HOH HOH . E 5 HOH A 8 308 22 HOH HOH . E 5 HOH A 9 309 60 HOH HOH . E 5 HOH A 10 310 111 HOH HOH . E 5 HOH A 11 311 85 HOH HOH . E 5 HOH A 12 312 68 HOH HOH . E 5 HOH A 13 313 84 HOH HOH . E 5 HOH A 14 314 115 HOH HOH . E 5 HOH A 15 315 44 HOH HOH . E 5 HOH A 16 316 74 HOH HOH . E 5 HOH A 17 317 41 HOH HOH . E 5 HOH A 18 318 7 HOH HOH . E 5 HOH A 19 319 3 HOH HOH . E 5 HOH A 20 320 2 HOH HOH . E 5 HOH A 21 321 40 HOH HOH . E 5 HOH A 22 322 130 HOH HOH . E 5 HOH A 23 323 87 HOH HOH . E 5 HOH A 24 324 46 HOH HOH . E 5 HOH A 25 325 102 HOH HOH . E 5 HOH A 26 326 126 HOH HOH . E 5 HOH A 27 327 65 HOH HOH . E 5 HOH A 28 328 64 HOH HOH . E 5 HOH A 29 329 50 HOH HOH . E 5 HOH A 30 330 110 HOH HOH . E 5 HOH A 31 331 30 HOH HOH . E 5 HOH A 32 332 79 HOH HOH . E 5 HOH A 33 333 101 HOH HOH . E 5 HOH A 34 334 77 HOH HOH . E 5 HOH A 35 335 80 HOH HOH . E 5 HOH A 36 336 95 HOH HOH . E 5 HOH A 37 337 42 HOH HOH . E 5 HOH A 38 338 8 HOH HOH . E 5 HOH A 39 339 113 HOH HOH . E 5 HOH A 40 340 11 HOH HOH . E 5 HOH A 41 341 14 HOH HOH . E 5 HOH A 42 342 16 HOH HOH . E 5 HOH A 43 343 107 HOH HOH . E 5 HOH A 44 344 98 HOH HOH . E 5 HOH A 45 345 89 HOH HOH . E 5 HOH A 46 346 71 HOH HOH . E 5 HOH A 47 347 55 HOH HOH . E 5 HOH A 48 348 72 HOH HOH . E 5 HOH A 49 349 54 HOH HOH . E 5 HOH A 50 350 59 HOH HOH . E 5 HOH A 51 351 83 HOH HOH . E 5 HOH A 52 352 4 HOH HOH . E 5 HOH A 53 353 38 HOH HOH . E 5 HOH A 54 354 93 HOH HOH . E 5 HOH A 55 355 97 HOH HOH . E 5 HOH A 56 356 57 HOH HOH . E 5 HOH A 57 357 36 HOH HOH . E 5 HOH A 58 358 15 HOH HOH . E 5 HOH A 59 359 73 HOH HOH . E 5 HOH A 60 360 21 HOH HOH . E 5 HOH A 61 361 104 HOH HOH . E 5 HOH A 62 362 48 HOH HOH . E 5 HOH A 63 363 88 HOH HOH . E 5 HOH A 64 364 27 HOH HOH . E 5 HOH A 65 365 86 HOH HOH . E 5 HOH A 66 366 28 HOH HOH . E 5 HOH A 67 367 76 HOH HOH . E 5 HOH A 68 368 56 HOH HOH . E 5 HOH A 69 369 1 HOH HOH . E 5 HOH A 70 370 39 HOH HOH . E 5 HOH A 71 371 92 HOH HOH . E 5 HOH A 72 372 31 HOH HOH . E 5 HOH A 73 373 63 HOH HOH . E 5 HOH A 74 374 114 HOH HOH . E 5 HOH A 75 375 139 HOH HOH . E 5 HOH A 76 376 37 HOH HOH . E 5 HOH A 77 377 26 HOH HOH . E 5 HOH A 78 378 47 HOH HOH . E 5 HOH A 79 379 90 HOH HOH . E 5 HOH A 80 380 33 HOH HOH . E 5 HOH A 81 381 12 HOH HOH . E 5 HOH A 82 382 20 HOH HOH . E 5 HOH A 83 383 138 HOH HOH . E 5 HOH A 84 384 127 HOH HOH . E 5 HOH A 85 385 106 HOH HOH . E 5 HOH A 86 386 62 HOH HOH . E 5 HOH A 87 387 25 HOH HOH . E 5 HOH A 88 388 6 HOH HOH . E 5 HOH A 89 389 124 HOH HOH . E 5 HOH A 90 390 96 HOH HOH . E 5 HOH A 91 391 17 HOH HOH . E 5 HOH A 92 392 122 HOH HOH . E 5 HOH A 93 393 99 HOH HOH . E 5 HOH A 94 394 43 HOH HOH . E 5 HOH A 95 395 51 HOH HOH . E 5 HOH A 96 396 116 HOH HOH . E 5 HOH A 97 397 9 HOH HOH . E 5 HOH A 98 398 34 HOH HOH . E 5 HOH A 99 399 35 HOH HOH . E 5 HOH A 100 400 123 HOH HOH . E 5 HOH A 101 401 18 HOH HOH . E 5 HOH A 102 402 128 HOH HOH . E 5 HOH A 103 403 24 HOH HOH . E 5 HOH A 104 404 23 HOH HOH . E 5 HOH A 105 405 29 HOH HOH . E 5 HOH A 106 406 108 HOH HOH . E 5 HOH A 107 407 5 HOH HOH . E 5 HOH A 108 408 69 HOH HOH . E 5 HOH A 109 409 94 HOH HOH . E 5 HOH A 110 410 19 HOH HOH . E 5 HOH A 111 411 100 HOH HOH . E 5 HOH A 112 412 53 HOH HOH . E 5 HOH A 113 413 136 HOH HOH . E 5 HOH A 114 414 133 HOH HOH . E 5 HOH A 115 415 91 HOH HOH . E 5 HOH A 116 416 32 HOH HOH . E 5 HOH A 117 417 137 HOH HOH . E 5 HOH A 118 418 129 HOH HOH . E 5 HOH A 119 419 135 HOH HOH . E 5 HOH A 120 420 118 HOH HOH . E 5 HOH A 121 421 75 HOH HOH . E 5 HOH A 122 422 45 HOH HOH . E 5 HOH A 123 423 49 HOH HOH . E 5 HOH A 124 424 67 HOH HOH . E 5 HOH A 125 425 141 HOH HOH . E 5 HOH A 126 426 140 HOH HOH . E 5 HOH A 127 427 119 HOH HOH . E 5 HOH A 128 428 125 HOH HOH . E 5 HOH A 129 429 66 HOH HOH . E 5 HOH A 130 430 121 HOH HOH . E 5 HOH A 131 431 58 HOH HOH . E 5 HOH A 132 432 78 HOH HOH . E 5 HOH A 133 433 120 HOH HOH . E 5 HOH A 134 434 82 HOH HOH . E 5 HOH A 135 435 81 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 R1N . . . C 3 2.113 28.034 32.373 0.5 19.54 ? C1 R1N 202 A 1 HETATM 2 C C2 R1N . . . C 3 1.998 26.379 30.454 0.5 19.91 ? C2 R1N 202 A 1 HETATM 3 C C3 R1N . . . C 3 2.67 30.135 33.647 0.5 20.72 ? C3 R1N 202 A 1 HETATM 4 C C4 R1N . . . C 3 3.271 29.655 31.292 0.5 19.85 ? C4 R1N 202 A 1 HETATM 5 C C5 R1N . . . C 3 3.1 28.602 30.402 0.5 19.53 ? C5 R1N 202 A 1 HETATM 6 C C6 R1N . . . C 3 3.576 28.665 29.092 0.5 20.98 ? C6 R1N 202 A 1 HETATM 7 C C7 R1N . . . C 3 4.264 29.822 28.743 0.5 21.84 ? C7 R1N 202 A 1 HETATM 8 C C8 R1N . . . C 3 4.442 30.872 29.648 0.5 21.87 ? C8 R1N 202 A 1 HETATM 9 C C9 R1N . . . C 3 3.945 30.816 30.947 0.5 21.28 ? C9 R1N 202 A 1 HETATM 10 C C10 R1N . . . C 3 2.894 26.086 34.543 0.5 22.84 ? C10 R1N 202 A 1 HETATM 11 C C11 R1N . . . C 3 4.279 26.527 34.191 0.5 23.61 ? C11 R1N 202 A 1 HETATM 12 C C12 R1N . . . C 3 2.158 25.023 33.941 0.5 22.65 ? C12 R1N 202 A 1 HETATM 13 C C13 R1N . . . C 3 2.67 24.103 32.88 0.5 22.16 ? C13 R1N 202 A 1 HETATM 14 C C14 R1N . . . C 3 0.891 24.881 34.63 0.5 21.94 ? C14 R1N 202 A 1 HETATM 15 C C15 R1N . . . C 3 -0.174 23.882 34.322 0.5 22.62 ? C15 R1N 202 A 1 HETATM 16 C C16 R1N . . . C 3 0.922 25.796 35.668 0.5 20.81 ? C16 R1N 202 A 1 HETATM 17 C C17 R1N . . . C 3 -0.107 25.733 36.743 0.5 11.48 ? C17 R1N 202 A 1 HETATM 18 C C18 R1N . . . C 3 2.09 26.631 35.596 0.5 21.48 ? C18 R1N 202 A 1 HETATM 19 C C19 R1N . . . C 3 2.487 27.67 36.606 0.5 23 ? C19 R1N 202 A 1 HETATM 20 N N1 R1N . . . C 3 2.389 27.636 31.092 0.5 20.28 ? N1 R1N 202 A 1 HETATM 21 N N2 R1N . . . C 3 2.667 29.269 32.486 0.5 20.77 ? N2 R1N 202 A 1 HETATM 22 CL CL1 R1N . . . C 3 -0.456 28.67 34.276 0.5 30.3 ? CL1 R1N 202 A 1 HETATM 23 RH RH R1N . . . C 3 1.08 26.887 33.719 0.5 22.2 ? RH R1N 202 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #