data_5ETV # _model_server_result.job_id yZ62yyq4dy6dxrJEixqBCA _model_server_result.datetime_utc '2024-11-22 13:48:56' _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 5etv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5ETV # _exptl.entry_id 5ETV _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 90 _cell.angle_gamma 120 _cell.entry_id 5ETV _cell.length_a 84.25 _cell.length_b 84.25 _cell.length_c 52.411 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ETV _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 _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 # 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 covale ? covale1 A C GLU 82 A GLU 79 1_555 A N CSO 83 A CSO 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C CSO 83 A CSO 80 1_555 A N LEU 84 A LEU 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD2 ASP 98 A ASP 95 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 A OD1 ASP 98 A ASP 95 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc3 A OD2 ASP 100 A ASP 97 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc4 A OD1 ASP 100 A ASP 97 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 B O1G APC . A APC 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc6 B O1B APC . A APC 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc7 B O1B APC . A APC 201 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc8 B O1A APC . A APC 201 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc9 D MG MG . A MG 203 1_555 G O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc10 D MG MG . A MG 203 1_555 G O HOH . A HOH 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 E MG MG . A MG 204 1_555 G O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc12 E MG MG . A MG 204 1_555 G O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? # _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 47 n n PG O2G APC sing 48 n n PG O3G APC sing 49 n n PG O3B APC sing 50 n n O2G HOG2 APC sing 51 n n O3G HOG3 APC sing 52 n n PB O1B APC doub 53 n n PB O2B APC sing 54 n n PB O3B APC sing 55 n n PB C3A APC sing 56 n n O2B HOB2 APC sing 57 n n PA O1A APC doub 58 n n PA O2A APC sing 59 n n PA C3A APC sing 60 n n PA O5' APC sing 61 n n O2A HOA2 APC sing 62 n n C3A H3A1 APC sing 63 n n C3A H3A2 APC sing 64 n n O5' C5' APC sing 65 n n C5' C4' APC sing 66 n n C5' "H5'1" APC sing 67 n n C5' "H5'2" APC sing 68 n n C4' O4' APC sing 69 n n C4' C3' APC sing 70 n n C4' H4' APC sing 71 n n O4' C1' APC sing 72 n n C3' O3' APC sing 73 n n C3' C2' APC sing 74 n n C3' H3' APC sing 75 n n O3' HO3' APC sing 76 n n C2' O2' APC sing 77 n n C2' C1' APC sing 78 n n C2' H2' APC sing 79 n n O2' HO2' APC sing 80 n n C1' N9 APC sing 81 n n C1' H1' APC sing 82 n n N9 C8 APC sing 83 n y N9 C4 APC sing 84 n y C8 N7 APC doub 85 n y C8 H8 APC sing 86 n n N7 C5 APC sing 87 n y C5 C6 APC sing 88 n y C5 C4 APC doub 89 n y C6 N6 APC sing 90 n n C6 N1 APC doub 91 n y N6 HN61 APC sing 92 n n N6 HN62 APC sing 93 n n N1 C2 APC sing 94 n y C2 N3 APC doub 95 n y C2 H2 APC sing 96 n n N3 C4 APC sing 97 n y # _atom_sites.entry_id 5ETV _atom_sites.fract_transf_matrix[1][1] 0.011869 _atom_sites.fract_transf_matrix[1][2] 0.006853 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013706 _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] 0.01908 _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 5RZ A 1 202 1 5RZ UNL . D 4 MG A 1 203 1 MG MG . E 4 MG A 1 204 2 MG MG . F 5 NO3 A 1 205 24 NO3 NO3 . G 6 HOH A 1 301 15 HOH HOH . G 6 HOH A 2 302 2 HOH HOH . G 6 HOH A 3 303 9 HOH HOH . G 6 HOH A 4 304 31 HOH HOH . G 6 HOH A 5 305 25 HOH HOH . G 6 HOH A 6 306 8 HOH HOH . G 6 HOH A 7 307 11 HOH HOH . G 6 HOH A 8 308 49 HOH HOH . G 6 HOH A 9 309 17 HOH HOH . G 6 HOH A 10 310 69 HOH HOH . G 6 HOH A 11 311 47 HOH HOH . G 6 HOH A 12 312 42 HOH HOH . G 6 HOH A 13 313 18 HOH HOH . G 6 HOH A 14 314 40 HOH HOH . G 6 HOH A 15 315 16 HOH HOH . G 6 HOH A 16 316 19 HOH HOH . G 6 HOH A 17 317 44 HOH HOH . G 6 HOH A 18 318 22 HOH HOH . G 6 HOH A 19 319 23 HOH HOH . G 6 HOH A 20 320 57 HOH HOH . G 6 HOH A 21 321 45 HOH HOH . G 6 HOH A 22 322 27 HOH HOH . G 6 HOH A 23 323 48 HOH HOH . G 6 HOH A 24 324 39 HOH HOH . G 6 HOH A 25 325 20 HOH HOH . G 6 HOH A 26 326 37 HOH HOH . G 6 HOH A 27 327 13 HOH HOH . G 6 HOH A 28 328 20 HOH HOH . G 6 HOH A 29 329 55 HOH HOH . G 6 HOH A 30 330 35 HOH HOH . G 6 HOH A 31 331 6 HOH HOH . G 6 HOH A 32 332 4 HOH HOH . G 6 HOH A 33 333 5 HOH HOH . G 6 HOH A 34 334 12 HOH HOH . G 6 HOH A 35 335 17 HOH HOH . G 6 HOH A 36 336 28 HOH HOH . G 6 HOH A 37 337 6 HOH HOH . G 6 HOH A 38 338 21 HOH HOH . G 6 HOH A 39 339 68 HOH HOH . G 6 HOH A 40 340 1 HOH HOH . G 6 HOH A 41 341 64 HOH HOH . G 6 HOH A 42 342 53 HOH HOH . G 6 HOH A 43 343 51 HOH HOH . G 6 HOH A 44 344 23 HOH HOH . G 6 HOH A 45 345 7 HOH HOH . G 6 HOH A 46 346 8 HOH HOH . G 6 HOH A 47 347 2 HOH HOH . G 6 HOH A 48 348 12 HOH HOH . G 6 HOH A 49 349 29 HOH HOH . G 6 HOH A 50 350 7 HOH HOH . G 6 HOH A 51 351 14 HOH HOH . G 6 HOH A 52 352 3 HOH HOH . G 6 HOH A 53 353 59 HOH HOH . G 6 HOH A 54 354 19 HOH HOH . G 6 HOH A 55 355 15 HOH HOH . G 6 HOH A 56 356 30 HOH HOH . G 6 HOH A 57 357 10 HOH HOH . G 6 HOH A 58 358 38 HOH HOH . G 6 HOH A 59 359 36 HOH HOH . G 6 HOH A 60 360 10 HOH HOH . G 6 HOH A 61 361 65 HOH HOH . G 6 HOH A 62 362 14 HOH HOH . G 6 HOH A 63 363 5 HOH HOH . G 6 HOH A 64 364 62 HOH HOH . G 6 HOH A 65 365 74 HOH HOH . G 6 HOH A 66 366 56 HOH HOH . G 6 HOH A 67 367 32 HOH HOH . G 6 HOH A 68 368 78 HOH HOH . G 6 HOH A 69 369 34 HOH HOH . G 6 HOH A 70 370 52 HOH HOH . G 6 HOH A 71 371 66 HOH HOH . G 6 HOH A 72 372 4 HOH HOH . G 6 HOH A 73 373 22 HOH HOH . G 6 HOH A 74 374 76 HOH HOH . G 6 HOH A 75 375 50 HOH HOH . G 6 HOH A 76 376 13 HOH HOH . G 6 HOH A 77 377 24 HOH HOH . G 6 HOH A 78 378 1 HOH HOH . G 6 HOH A 79 379 54 HOH HOH . G 6 HOH A 80 380 61 HOH HOH . G 6 HOH A 81 381 46 HOH HOH . G 6 HOH A 82 382 16 HOH HOH . G 6 HOH A 83 383 72 HOH HOH . G 6 HOH A 84 384 3 HOH HOH . G 6 HOH A 85 385 67 HOH HOH . G 6 HOH A 86 386 63 HOH HOH . G 6 HOH A 87 387 41 HOH HOH . G 6 HOH A 88 388 33 HOH HOH . G 6 HOH A 89 389 26 HOH HOH . G 6 HOH A 90 390 11 HOH HOH . G 6 HOH A 91 391 21 HOH HOH . G 6 HOH A 92 392 71 HOH HOH . G 6 HOH A 93 393 43 HOH HOH . G 6 HOH A 94 394 18 HOH HOH . G 6 HOH A 95 395 77 HOH HOH . G 6 HOH A 96 396 75 HOH HOH . G 6 HOH A 97 397 9 HOH HOH . G 6 HOH A 98 398 73 HOH HOH . G 6 HOH A 99 399 58 HOH HOH . G 6 HOH A 100 400 70 HOH HOH . G 6 HOH A 101 401 60 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 -9.822 45.6 19.409 1 12.18 ? PG APC 201 A 1 HETATM 2 O O1G APC . . . B 2 -10.716 44.62 18.703 1 11.28 ? O1G APC 201 A 1 HETATM 3 O O2G APC . . . B 2 -9.882 47.011 18.908 1 12.46 ? O2G APC 201 A 1 HETATM 4 O O3G APC . . . B 2 -8.44 45.045 19.63 1 10.77 ? O3G APC 201 A 1 HETATM 5 P PB APC . . . B 2 -11.806 46.25 21.326 1 13.14 ? PB APC 201 A 1 HETATM 6 O O1B APC . . . B 2 -12.652 46.402 20.075 1 13.05 ? O1B APC 201 A 1 HETATM 7 O O2B APC . . . B 2 -12.406 45.33 22.473 1 14.19 ? O2B APC 201 A 1 HETATM 8 O O3B APC . . . B 2 -10.366 45.673 20.944 1 11.92 ? O3B APC 201 A 1 HETATM 9 P PA APC . . . B 2 -12.847 48.944 22.246 1 14.19 ? PA APC 201 A 1 HETATM 10 O O1A APC . . . B 2 -13.994 48.645 21.233 1 12.06 ? O1A APC 201 A 1 HETATM 11 O O2A APC . . . B 2 -13.283 48.798 23.667 1 15.85 ? O2A APC 201 A 1 HETATM 12 C C3A APC . . . B 2 -11.416 47.9 21.967 1 12.62 ? C3A APC 201 A 1 HETATM 13 O O5' APC . . . B 2 -12.477 50.45 21.797 1 15.98 ? O5' APC 201 A 1 HETATM 14 C C5' APC . . . B 2 -11.495 51.208 22.427 1 20.96 ? C5' APC 201 A 1 HETATM 15 C C4' APC . . . B 2 -10.909 52.234 21.468 1 17.06 ? C4' APC 201 A 1 HETATM 16 O O4' APC . . . B 2 -10.146 51.544 20.465 1 16.2 ? O4' APC 201 A 1 HETATM 17 C C3' APC . . . B 2 -11.783 53.168 20.652 1 20.88 ? C3' APC 201 A 1 HETATM 18 O O3' APC . . . B 2 -12.344 54.239 21.404 1 18.82 ? O3' APC 201 A 1 HETATM 19 C C2' APC . . . B 2 -10.761 53.675 19.655 1 22.2 ? C2' APC 201 A 1 HETATM 20 O O2' APC . . . B 2 -10.198 54.928 20.105 1 25.77 ? O2' APC 201 A 1 HETATM 21 C C1' APC . . . B 2 -9.683 52.603 19.657 1 16.69 ? C1' APC 201 A 1 HETATM 22 N N9 APC . . . B 2 -9.337 52.126 18.311 1 16.86 ? N9 APC 201 A 1 HETATM 23 C C8 APC . . . B 2 -8.098 52.133 17.793 1 19.49 ? C8 APC 201 A 1 HETATM 24 N N7 APC . . . B 2 -8.126 51.678 16.501 1 17.33 ? N7 APC 201 A 1 HETATM 25 C C5 APC . . . B 2 -9.42 51.337 16.225 1 14.65 ? C5 APC 201 A 1 HETATM 26 C C6 APC . . . B 2 -10.12 50.772 15.065 1 14.19 ? C6 APC 201 A 1 HETATM 27 N N6 APC . . . B 2 -9.359 50.511 13.962 1 12.66 ? N6 APC 201 A 1 HETATM 28 N N1 APC . . . B 2 -11.459 50.581 15.171 1 13.72 ? N1 APC 201 A 1 HETATM 29 C C2 APC . . . B 2 -12.147 50.871 16.312 1 14.49 ? C2 APC 201 A 1 HETATM 30 N N3 APC . . . B 2 -11.556 51.394 17.419 1 14.51 ? N3 APC 201 A 1 HETATM 31 C C4 APC . . . B 2 -10.224 51.637 17.423 1 15.23 ? C4 APC 201 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 384 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 31 #