data_6VCO # _model_server_result.job_id rFu-aPcfDch0Y4lv7XLo7w _model_server_result.datetime_utc '2024-11-12 20:34:58' _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 6vco # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6VCO # _exptl.entry_id 6VCO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 100.064 _cell.angle_gamma 90 _cell.entry_id 6VCO _cell.length_a 79.14 _cell.length_b 38.955 _cell.length_c 57.734 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VCO _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 6VCO _atom_sites.fract_transf_matrix[1][1] 0.012636 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002243 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025671 _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] 0.017591 _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 APC A 1 201 1 APC APC . C 3 HOH A 1 301 93 HOH HOH . C 3 HOH A 2 302 51 HOH HOH . C 3 HOH A 3 303 58 HOH HOH . C 3 HOH A 4 304 15 HOH HOH . C 3 HOH A 5 305 86 HOH HOH . C 3 HOH A 6 306 66 HOH HOH . C 3 HOH A 7 307 108 HOH HOH . C 3 HOH A 8 308 103 HOH HOH . C 3 HOH A 9 309 77 HOH HOH . C 3 HOH A 10 310 80 HOH HOH . C 3 HOH A 11 311 70 HOH HOH . C 3 HOH A 12 312 112 HOH HOH . C 3 HOH A 13 313 44 HOH HOH . C 3 HOH A 14 314 12 HOH HOH . C 3 HOH A 15 315 59 HOH HOH . C 3 HOH A 16 316 41 HOH HOH . C 3 HOH A 17 317 23 HOH HOH . C 3 HOH A 18 318 78 HOH HOH . C 3 HOH A 19 319 61 HOH HOH . C 3 HOH A 20 320 72 HOH HOH . C 3 HOH A 21 321 14 HOH HOH . C 3 HOH A 22 322 131 HOH HOH . C 3 HOH A 23 323 47 HOH HOH . C 3 HOH A 24 324 153 HOH HOH . C 3 HOH A 25 325 19 HOH HOH . C 3 HOH A 26 326 73 HOH HOH . C 3 HOH A 27 327 106 HOH HOH . C 3 HOH A 28 328 45 HOH HOH . C 3 HOH A 29 329 107 HOH HOH . C 3 HOH A 30 330 33 HOH HOH . C 3 HOH A 31 331 157 HOH HOH . C 3 HOH A 32 332 7 HOH HOH . C 3 HOH A 33 333 117 HOH HOH . C 3 HOH A 34 334 114 HOH HOH . C 3 HOH A 35 335 35 HOH HOH . C 3 HOH A 36 336 5 HOH HOH . C 3 HOH A 37 337 13 HOH HOH . C 3 HOH A 38 338 25 HOH HOH . C 3 HOH A 39 339 79 HOH HOH . C 3 HOH A 40 340 54 HOH HOH . C 3 HOH A 41 341 56 HOH HOH . C 3 HOH A 42 342 10 HOH HOH . C 3 HOH A 43 343 6 HOH HOH . C 3 HOH A 44 344 99 HOH HOH . C 3 HOH A 45 345 11 HOH HOH . C 3 HOH A 46 346 55 HOH HOH . C 3 HOH A 47 347 120 HOH HOH . C 3 HOH A 48 348 141 HOH HOH . C 3 HOH A 49 349 8 HOH HOH . C 3 HOH A 50 350 88 HOH HOH . C 3 HOH A 51 351 152 HOH HOH . C 3 HOH A 52 352 119 HOH HOH . C 3 HOH A 53 353 138 HOH HOH . C 3 HOH A 54 354 28 HOH HOH . C 3 HOH A 55 355 69 HOH HOH . C 3 HOH A 56 356 68 HOH HOH . C 3 HOH A 57 357 115 HOH HOH . C 3 HOH A 58 358 48 HOH HOH . C 3 HOH A 59 359 17 HOH HOH . C 3 HOH A 60 360 161 HOH HOH . C 3 HOH A 61 361 136 HOH HOH . C 3 HOH A 62 362 29 HOH HOH . C 3 HOH A 63 363 1 HOH HOH . C 3 HOH A 64 364 128 HOH HOH . C 3 HOH A 65 365 83 HOH HOH . C 3 HOH A 66 366 81 HOH HOH . C 3 HOH A 67 367 60 HOH HOH . C 3 HOH A 68 368 16 HOH HOH . C 3 HOH A 69 369 3 HOH HOH . C 3 HOH A 70 370 163 HOH HOH . C 3 HOH A 71 371 95 HOH HOH . C 3 HOH A 72 372 134 HOH HOH . C 3 HOH A 73 373 37 HOH HOH . C 3 HOH A 74 374 71 HOH HOH . C 3 HOH A 75 375 52 HOH HOH . C 3 HOH A 76 376 46 HOH HOH . C 3 HOH A 77 377 154 HOH HOH . C 3 HOH A 78 378 24 HOH HOH . C 3 HOH A 79 379 32 HOH HOH . C 3 HOH A 80 380 2 HOH HOH . C 3 HOH A 81 381 135 HOH HOH . C 3 HOH A 82 382 145 HOH HOH . C 3 HOH A 83 383 126 HOH HOH . C 3 HOH A 84 384 9 HOH HOH . C 3 HOH A 85 385 57 HOH HOH . C 3 HOH A 86 386 159 HOH HOH . C 3 HOH A 87 387 91 HOH HOH . C 3 HOH A 88 388 63 HOH HOH . C 3 HOH A 89 389 38 HOH HOH . C 3 HOH A 90 390 101 HOH HOH . C 3 HOH A 91 391 144 HOH HOH . C 3 HOH A 92 392 169 HOH HOH . C 3 HOH A 93 393 74 HOH HOH . C 3 HOH A 94 394 165 HOH HOH . C 3 HOH A 95 395 132 HOH HOH . C 3 HOH A 96 396 26 HOH HOH . C 3 HOH A 97 397 64 HOH HOH . C 3 HOH A 98 398 18 HOH HOH . C 3 HOH A 99 399 65 HOH HOH . C 3 HOH A 100 400 20 HOH HOH . C 3 HOH A 101 401 82 HOH HOH . C 3 HOH A 102 402 133 HOH HOH . C 3 HOH A 103 403 4 HOH HOH . C 3 HOH A 104 404 85 HOH HOH . C 3 HOH A 105 405 102 HOH HOH . C 3 HOH A 106 406 36 HOH HOH . C 3 HOH A 107 407 21 HOH HOH . C 3 HOH A 108 408 113 HOH HOH . C 3 HOH A 109 409 42 HOH HOH . C 3 HOH A 110 410 34 HOH HOH . C 3 HOH A 111 411 22 HOH HOH . C 3 HOH A 112 412 92 HOH HOH . C 3 HOH A 113 413 31 HOH HOH . C 3 HOH A 114 414 122 HOH HOH . C 3 HOH A 115 415 96 HOH HOH . C 3 HOH A 116 416 76 HOH HOH . C 3 HOH A 117 417 168 HOH HOH . C 3 HOH A 118 418 49 HOH HOH . C 3 HOH A 119 419 147 HOH HOH . C 3 HOH A 120 420 158 HOH HOH . C 3 HOH A 121 421 109 HOH HOH . C 3 HOH A 122 422 140 HOH HOH . C 3 HOH A 123 423 166 HOH HOH . C 3 HOH A 124 424 111 HOH HOH . C 3 HOH A 125 425 129 HOH HOH . C 3 HOH A 126 426 105 HOH HOH . C 3 HOH A 127 427 27 HOH HOH . C 3 HOH A 128 428 167 HOH HOH . C 3 HOH A 129 429 30 HOH HOH . C 3 HOH A 130 430 104 HOH HOH . C 3 HOH A 131 431 137 HOH HOH . C 3 HOH A 132 432 40 HOH HOH . C 3 HOH A 133 433 146 HOH HOH . C 3 HOH A 134 434 121 HOH HOH . C 3 HOH A 135 435 164 HOH HOH . C 3 HOH A 136 436 118 HOH HOH . C 3 HOH A 137 437 43 HOH HOH . C 3 HOH A 138 438 50 HOH HOH . C 3 HOH A 139 439 162 HOH HOH . C 3 HOH A 140 440 139 HOH HOH . C 3 HOH A 141 441 87 HOH HOH . C 3 HOH A 142 442 98 HOH HOH . C 3 HOH A 143 443 62 HOH HOH . C 3 HOH A 144 444 39 HOH HOH . C 3 HOH A 145 445 97 HOH HOH . C 3 HOH A 146 446 75 HOH HOH . C 3 HOH A 147 447 151 HOH HOH . C 3 HOH A 148 448 84 HOH HOH . C 3 HOH A 149 449 127 HOH HOH . C 3 HOH A 150 450 150 HOH HOH . C 3 HOH A 151 451 123 HOH HOH . C 3 HOH A 152 452 110 HOH HOH . C 3 HOH A 153 453 100 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 P PG APC . . . B 2 27.262 1.564 12.944 1 68.1 ? PG APC 201 A 1 HETATM 2 O O1G APC . . . B 2 26.091 2.356 12.374 1 60.78 ? O1G APC 201 A 1 HETATM 3 O O2G APC . . . B 2 27.508 1.956 14.385 1 67.34 ? O2G APC 201 A 1 HETATM 4 O O3G APC . . . B 2 28.578 1.767 12.129 1 68.3 ? O3G APC 201 A 1 HETATM 5 P PB APC . . . B 2 26.779 -1.04 14.142 1 36.59 ? PB APC 201 A 1 HETATM 6 O O1B APC . . . B 2 26.138 -2.316 13.627 1 35.65 ? O1B APC 201 A 1 HETATM 7 O O2B APC . . . B 2 28.192 -1.36 14.722 1 43.45 ? O2B APC 201 A 1 HETATM 8 O O3B APC . . . B 2 26.879 0.015 12.962 1 52.32 ? O3B APC 201 A 1 HETATM 9 P PA APC . . . B 2 25.005 -1.432 16.668 1 32.46 ? PA APC 201 A 1 HETATM 10 O O1A APC . . . B 2 24.65 -0.692 17.927 1 28.68 ? O1A APC 201 A 1 HETATM 11 O O2A APC . . . B 2 23.817 -2.182 16.005 1 28.97 ? O2A APC 201 A 1 HETATM 12 C C3A APC . . . B 2 25.751 -0.215 15.513 1 38.52 ? C3A APC 201 A 1 HETATM 13 O O5' APC . . . B 2 26.113 -2.508 16.99 1 33.77 ? O5' APC 201 A 1 HETATM 14 C C5' APC . . . B 2 27.257 -2.168 17.878 1 38.51 ? C5' APC 201 A 1 HETATM 15 C C4' APC . . . B 2 28.097 -3.424 17.946 1 39.17 ? C4' APC 201 A 1 HETATM 16 O O4' APC . . . B 2 27.217 -4.444 18.483 1 33.72 ? O4' APC 201 A 1 HETATM 17 C C3' APC . . . B 2 28.494 -3.921 16.614 1 43.23 ? C3' APC 201 A 1 HETATM 18 O O3' APC . . . B 2 29.896 -3.781 16.36 1 58.14 ? O3' APC 201 A 1 HETATM 19 C C2' APC . . . B 2 28.05 -5.398 16.685 1 44.55 ? C2' APC 201 A 1 HETATM 20 O O2' APC . . . B 2 29.178 -6.258 16.535 1 55.43 ? O2' APC 201 A 1 HETATM 21 C C1' APC . . . B 2 27.454 -5.664 17.82 1 36.85 ? C1' APC 201 A 1 HETATM 22 N N9 APC . . . B 2 26.193 -6.333 17.504 1 41.94 ? N9 APC 201 A 1 HETATM 23 C C8 APC . . . B 2 25.052 -5.732 17.054 1 35.08 ? C8 APC 201 A 1 HETATM 24 N N7 APC . . . B 2 24.042 -6.594 16.817 1 36.02 ? N7 APC 201 A 1 HETATM 25 C C5 APC . . . B 2 24.612 -7.815 17.166 1 37.22 ? C5 APC 201 A 1 HETATM 26 C C6 APC . . . B 2 24.086 -9.108 17.135 1 35.22 ? C6 APC 201 A 1 HETATM 27 N N6 APC . . . B 2 22.817 -9.352 16.771 1 40.27 ? N6 APC 201 A 1 HETATM 28 N N1 APC . . . B 2 24.785 -10.115 17.512 1 42.3 ? N1 APC 201 A 1 HETATM 29 C C2 APC . . . B 2 26.051 -9.867 17.9 1 43.3 ? C2 APC 201 A 1 HETATM 30 N N3 APC . . . B 2 26.654 -8.714 17.965 1 47.41 ? N3 APC 201 A 1 HETATM 31 C C4 APC . . . B 2 25.924 -7.631 17.587 1 37.37 ? C4 APC 201 A 1 HETATM 32 H H3A1 APC . . . B 2 26.326 0.379 16.02 1 46.22 ? H3A1 APC 201 A 1 HETATM 33 H H3A2 APC . . . B 2 25.038 0.298 15.102 1 46.22 ? H3A2 APC 201 A 1 HETATM 34 H "H5'1" APC . . . B 2 26.942 -1.923 18.762 1 46.21 ? "H5'1" APC 201 A 1 HETATM 35 H "H5'2" APC . . . B 2 27.773 -1.436 17.504 1 46.21 ? "H5'2" APC 201 A 1 HETATM 36 H H4' APC . . . B 2 28.909 -3.287 18.458 1 47 ? H4' APC 201 A 1 HETATM 37 H H3' APC . . . B 2 28.043 -3.438 15.903 1 51.87 ? H3' APC 201 A 1 HETATM 38 H HO3' APC . . . B 2 29.986 -3.523 15.542 1 69.76 ? HO3' APC 201 A 1 HETATM 39 H H2' APC . . . B 2 27.372 -5.518 16.001 1 53.46 ? H2' APC 201 A 1 HETATM 40 H HO2' APC . . . B 2 29.261 -6.516 15.758 1 66.51 ? HO2' APC 201 A 1 HETATM 41 H H1' APC . . . B 2 28.027 -6.197 18.393 1 44.22 ? H1' APC 201 A 1 HETATM 42 H H8 APC . . . B 2 24.98 -4.814 16.924 1 42.1 ? H8 APC 201 A 1 HETATM 43 H HN61 APC . . . B 2 22.466 -10.146 16.99 1 48.32 ? HN61 APC 201 A 1 HETATM 44 H HN62 APC . . . B 2 22.414 -8.712 16.396 1 48.32 ? HN62 APC 201 A 1 HETATM 45 H H2 APC . . . B 2 26.572 -10.63 18.176 1 51.95 ? H2 APC 201 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #