data_3T25 # _model_server_result.job_id ojIuiW8iikraPA2vNScCLQ _model_server_result.datetime_utc '2024-11-05 13:42:12' _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 3t25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":251}' # _entry.id 3T25 # _exptl.entry_id 3T25 _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 90 _cell.entry_id 3T25 _cell.length_a 54.934 _cell.length_b 58.576 _cell.length_c 67.941 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T25 _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 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 _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 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc1 A OE1 GLU 52 A GLU 70 1_555 B CA CA . A CA 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc5 B CA CA . A CA 246 1_555 H O HOH . A HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc6 B CA CA . A CA 246 1_555 H O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? # _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 3T25 _atom_sites.fract_transf_matrix[1][1] 0.018204 _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] 0.017072 _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] 0.014719 _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 CA A 1 246 246 CA CA . C 3 SO4 A 1 247 247 SO4 SO4 . D 4 BEN A 1 251 251 BEN BEN . E 5 TMO A 1 261 261 TMO TMO . F 5 TMO A 1 262 262 TMO TMO . G 5 TMO A 1 266 266 TMO TMO . H 6 HOH A 1 301 301 HOH HOH . H 6 HOH A 2 302 302 HOH HOH . H 6 HOH A 3 303 303 HOH HOH . H 6 HOH A 4 304 304 HOH HOH . H 6 HOH A 5 305 305 HOH HOH . H 6 HOH A 6 306 306 HOH HOH . H 6 HOH A 7 307 307 HOH HOH . H 6 HOH A 8 308 308 HOH HOH . H 6 HOH A 9 309 309 HOH HOH . H 6 HOH A 10 310 310 HOH HOH . H 6 HOH A 11 311 311 HOH HOH . H 6 HOH A 12 312 312 HOH HOH . H 6 HOH A 13 313 313 HOH HOH . H 6 HOH A 14 314 314 HOH HOH . H 6 HOH A 15 315 315 HOH HOH . H 6 HOH A 16 316 316 HOH HOH . H 6 HOH A 17 317 317 HOH HOH . H 6 HOH A 18 318 318 HOH HOH . H 6 HOH A 19 319 319 HOH HOH . H 6 HOH A 20 320 320 HOH HOH . H 6 HOH A 21 321 321 HOH HOH . H 6 HOH A 22 322 322 HOH HOH . H 6 HOH A 23 323 323 HOH HOH . H 6 HOH A 24 324 324 HOH HOH . H 6 HOH A 25 325 325 HOH HOH . H 6 HOH A 26 326 326 HOH HOH . H 6 HOH A 27 327 327 HOH HOH . H 6 HOH A 28 328 328 HOH HOH . H 6 HOH A 29 329 329 HOH HOH . H 6 HOH A 30 330 330 HOH HOH . H 6 HOH A 31 331 331 HOH HOH . H 6 HOH A 32 332 332 HOH HOH . H 6 HOH A 33 333 333 HOH HOH . H 6 HOH A 34 334 334 HOH HOH . H 6 HOH A 35 335 335 HOH HOH . H 6 HOH A 36 336 336 HOH HOH . H 6 HOH A 37 337 337 HOH HOH . H 6 HOH A 38 338 338 HOH HOH . H 6 HOH A 39 339 339 HOH HOH . H 6 HOH A 40 340 340 HOH HOH . H 6 HOH A 41 341 341 HOH HOH . H 6 HOH A 42 342 342 HOH HOH . H 6 HOH A 43 343 343 HOH HOH . H 6 HOH A 44 344 344 HOH HOH . H 6 HOH A 45 345 345 HOH HOH . H 6 HOH A 46 346 346 HOH HOH . H 6 HOH A 47 347 347 HOH HOH . H 6 HOH A 48 348 348 HOH HOH . H 6 HOH A 49 349 349 HOH HOH . H 6 HOH A 50 350 350 HOH HOH . H 6 HOH A 51 351 351 HOH HOH . H 6 HOH A 52 352 352 HOH HOH . H 6 HOH A 53 353 353 HOH HOH . H 6 HOH A 54 354 354 HOH HOH . H 6 HOH A 55 355 355 HOH HOH . H 6 HOH A 56 356 356 HOH HOH . H 6 HOH A 57 357 357 HOH HOH . H 6 HOH A 58 358 358 HOH HOH . H 6 HOH A 59 359 359 HOH HOH . H 6 HOH A 60 360 360 HOH HOH . H 6 HOH A 61 361 361 HOH HOH . H 6 HOH A 62 362 362 HOH HOH . H 6 HOH A 63 363 363 HOH HOH . H 6 HOH A 64 364 364 HOH HOH . H 6 HOH A 65 365 365 HOH HOH . H 6 HOH A 66 366 366 HOH HOH . H 6 HOH A 67 367 367 HOH HOH . H 6 HOH A 68 368 368 HOH HOH . H 6 HOH A 69 369 369 HOH HOH . H 6 HOH A 70 370 370 HOH HOH . H 6 HOH A 71 371 371 HOH HOH . H 6 HOH A 72 372 372 HOH HOH . H 6 HOH A 73 373 373 HOH HOH . H 6 HOH A 74 374 374 HOH HOH . H 6 HOH A 75 375 375 HOH HOH . H 6 HOH A 76 376 376 HOH HOH . H 6 HOH A 77 377 377 HOH HOH . H 6 HOH A 78 378 378 HOH HOH . H 6 HOH A 79 379 379 HOH HOH . H 6 HOH A 80 380 380 HOH HOH . H 6 HOH A 81 381 381 HOH HOH . H 6 HOH A 82 382 382 HOH HOH . H 6 HOH A 83 383 383 HOH HOH . H 6 HOH A 84 384 384 HOH HOH . H 6 HOH A 85 385 385 HOH HOH . H 6 HOH A 86 386 386 HOH HOH . H 6 HOH A 87 387 387 HOH HOH . H 6 HOH A 88 388 388 HOH HOH . H 6 HOH A 89 389 389 HOH HOH . H 6 HOH A 90 390 390 HOH HOH . H 6 HOH A 91 391 391 HOH HOH . H 6 HOH A 92 392 392 HOH HOH . H 6 HOH A 93 393 393 HOH HOH . H 6 HOH A 94 394 394 HOH HOH . H 6 HOH A 95 395 395 HOH HOH . H 6 HOH A 96 396 396 HOH HOH . H 6 HOH A 97 397 397 HOH HOH . H 6 HOH A 98 398 398 HOH HOH . H 6 HOH A 99 399 399 HOH HOH . H 6 HOH A 100 400 400 HOH HOH . H 6 HOH A 101 401 401 HOH HOH . H 6 HOH A 102 402 402 HOH HOH . H 6 HOH A 103 403 403 HOH HOH . H 6 HOH A 104 404 404 HOH HOH . H 6 HOH A 105 405 405 HOH HOH . H 6 HOH A 106 406 406 HOH HOH . H 6 HOH A 107 407 407 HOH HOH . H 6 HOH A 108 408 408 HOH HOH . H 6 HOH A 109 409 409 HOH HOH . H 6 HOH A 110 410 410 HOH HOH . H 6 HOH A 111 411 411 HOH HOH . H 6 HOH A 112 412 412 HOH HOH . H 6 HOH A 113 413 413 HOH HOH . H 6 HOH A 114 414 414 HOH HOH . H 6 HOH A 115 415 415 HOH HOH . H 6 HOH A 116 416 416 HOH HOH . H 6 HOH A 117 417 417 HOH HOH . H 6 HOH A 118 418 418 HOH HOH . H 6 HOH A 119 419 419 HOH HOH . H 6 HOH A 120 420 420 HOH HOH . H 6 HOH A 121 421 421 HOH HOH . H 6 HOH A 122 422 422 HOH HOH . H 6 HOH A 123 423 423 HOH HOH . H 6 HOH A 124 424 424 HOH HOH . H 6 HOH A 125 425 425 HOH HOH . H 6 HOH A 126 426 426 HOH HOH . H 6 HOH A 127 427 427 HOH HOH . H 6 HOH A 128 428 428 HOH HOH . H 6 HOH A 129 429 429 HOH HOH . H 6 HOH A 130 430 430 HOH HOH . H 6 HOH A 131 431 431 HOH HOH . H 6 HOH A 132 432 432 HOH HOH . H 6 HOH A 133 433 433 HOH HOH . H 6 HOH A 134 434 434 HOH HOH . H 6 HOH A 135 435 435 HOH HOH . H 6 HOH A 136 436 436 HOH HOH . H 6 HOH A 137 437 437 HOH HOH . H 6 HOH A 138 438 438 HOH HOH . H 6 HOH A 139 439 439 HOH HOH . H 6 HOH A 140 440 440 HOH HOH . H 6 HOH A 141 441 441 HOH HOH . H 6 HOH A 142 442 442 HOH HOH . H 6 HOH A 143 443 443 HOH HOH . H 6 HOH A 144 444 444 HOH HOH . H 6 HOH A 145 445 445 HOH HOH . H 6 HOH A 146 446 446 HOH HOH . H 6 HOH A 147 447 447 HOH HOH . H 6 HOH A 148 448 448 HOH HOH . H 6 HOH A 149 449 449 HOH HOH . H 6 HOH A 150 450 450 HOH HOH . H 6 HOH A 151 451 451 HOH HOH . H 6 HOH A 152 452 452 HOH HOH . H 6 HOH A 153 453 453 HOH HOH . H 6 HOH A 154 454 454 HOH HOH . H 6 HOH A 155 455 455 HOH HOH . H 6 HOH A 156 456 456 HOH HOH . H 6 HOH A 157 457 457 HOH HOH . H 6 HOH A 158 458 458 HOH HOH . H 6 HOH A 159 459 459 HOH HOH . H 6 HOH A 160 460 460 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 -1.815 14.417 16.785 1 11.92 ? C1 BEN 251 A 1 HETATM 2 C C2 BEN . . . D 4 -1.257 13.796 17.889 1 12.97 ? C2 BEN 251 A 1 HETATM 3 C C3 BEN . . . D 4 -0.938 14.497 19.055 1 15.11 ? C3 BEN 251 A 1 HETATM 4 C C4 BEN . . . D 4 -1.146 15.866 19.095 1 14.39 ? C4 BEN 251 A 1 HETATM 5 C C5 BEN . . . D 4 -1.674 16.528 17.984 1 15.76 ? C5 BEN 251 A 1 HETATM 6 C C6 BEN . . . D 4 -2.027 15.813 16.838 1 13.75 ? C6 BEN 251 A 1 HETATM 7 C C BEN . . . D 4 -2.131 13.673 15.636 1 11.39 ? C BEN 251 A 1 HETATM 8 N N1 BEN . . . D 4 -1.769 12.389 15.492 1 10.24 ? N1 BEN 251 A 1 HETATM 9 N N2 BEN . . . D 4 -2.834 14.194 14.642 1 12.29 ? N2 BEN 251 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 9 #