data_3BD9 # _model_server_result.job_id V2cWLKeeswgSBBJhhf1Lqg _model_server_result.datetime_utc '2024-11-26 05:46:49' _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 3bd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":347}' # _entry.id 3BD9 # _exptl.entry_id 3BD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'A3P procured from Sigma' _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 3BD9 _cell.length_a 59.27 _cell.length_b 59.27 _cell.length_c 173.957 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BD9 _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 _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 228 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 294 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 238 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 304 _struct_conn.ptnr2_symmetry 1_555 _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 2.04 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3BD9 _atom_sites.fract_transf_matrix[1][1] 0.016872 _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] 0.016872 _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] 0.005749 _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 A3P A 1 347 347 A3P A3P . C 3 HOH A 1 348 348 HOH HOH . C 3 HOH A 2 349 349 HOH HOH . C 3 HOH A 3 350 350 HOH HOH . C 3 HOH A 4 351 351 HOH HOH . C 3 HOH A 5 352 352 HOH HOH . C 3 HOH A 6 353 353 HOH HOH . C 3 HOH A 7 354 354 HOH HOH . C 3 HOH A 8 355 355 HOH HOH . C 3 HOH A 9 356 356 HOH HOH . C 3 HOH A 10 357 357 HOH HOH . C 3 HOH A 11 358 358 HOH HOH . C 3 HOH A 12 359 359 HOH HOH . C 3 HOH A 13 360 360 HOH HOH . C 3 HOH A 14 361 361 HOH HOH . C 3 HOH A 15 362 362 HOH HOH . C 3 HOH A 16 363 363 HOH HOH . C 3 HOH A 17 364 364 HOH HOH . C 3 HOH A 18 365 365 HOH HOH . C 3 HOH A 19 366 366 HOH HOH . C 3 HOH A 20 367 367 HOH HOH . C 3 HOH A 21 368 368 HOH HOH . C 3 HOH A 22 369 369 HOH HOH . C 3 HOH A 23 370 370 HOH HOH . C 3 HOH A 24 371 371 HOH HOH . C 3 HOH A 25 372 372 HOH HOH . C 3 HOH A 26 373 373 HOH HOH . C 3 HOH A 27 374 374 HOH HOH . C 3 HOH A 28 375 375 HOH HOH . C 3 HOH A 29 376 376 HOH HOH . C 3 HOH A 30 377 377 HOH HOH . C 3 HOH A 31 378 378 HOH HOH . C 3 HOH A 32 379 379 HOH HOH . C 3 HOH A 33 380 380 HOH HOH . C 3 HOH A 34 381 381 HOH HOH . C 3 HOH A 35 382 382 HOH HOH . C 3 HOH A 36 383 383 HOH HOH . C 3 HOH A 37 384 384 HOH HOH . C 3 HOH A 38 385 385 HOH HOH . C 3 HOH A 39 386 386 HOH HOH . C 3 HOH A 40 387 387 HOH HOH . C 3 HOH A 41 388 388 HOH HOH . C 3 HOH A 42 389 389 HOH HOH . C 3 HOH A 43 390 390 HOH HOH . C 3 HOH A 44 391 391 HOH HOH . C 3 HOH A 45 392 392 HOH HOH . C 3 HOH A 46 393 393 HOH HOH . C 3 HOH A 47 394 394 HOH HOH . C 3 HOH A 48 395 395 HOH HOH . C 3 HOH A 49 396 396 HOH HOH . C 3 HOH A 50 397 397 HOH HOH . C 3 HOH A 51 398 398 HOH HOH . C 3 HOH A 52 399 399 HOH HOH . C 3 HOH A 53 400 400 HOH HOH . C 3 HOH A 54 401 401 HOH HOH . C 3 HOH A 55 402 402 HOH HOH . C 3 HOH A 56 403 403 HOH HOH . C 3 HOH A 57 404 404 HOH HOH . C 3 HOH A 58 405 405 HOH HOH . C 3 HOH A 59 406 406 HOH HOH . C 3 HOH A 60 407 407 HOH HOH . C 3 HOH A 61 408 408 HOH HOH . C 3 HOH A 62 409 409 HOH HOH . C 3 HOH A 63 410 410 HOH HOH . C 3 HOH A 64 411 411 HOH HOH . C 3 HOH A 65 412 412 HOH HOH . C 3 HOH A 66 413 413 HOH HOH . C 3 HOH A 67 414 414 HOH HOH . C 3 HOH A 68 415 415 HOH HOH . C 3 HOH A 69 416 416 HOH HOH . C 3 HOH A 70 417 417 HOH HOH . C 3 HOH A 71 418 418 HOH HOH . C 3 HOH A 72 419 419 HOH HOH . C 3 HOH A 73 420 420 HOH HOH . C 3 HOH A 74 421 421 HOH HOH . C 3 HOH A 75 422 422 HOH HOH . C 3 HOH A 76 423 423 HOH HOH . C 3 HOH A 77 424 424 HOH HOH . C 3 HOH A 78 425 425 HOH HOH . C 3 HOH A 79 426 426 HOH HOH . C 3 HOH A 80 427 427 HOH HOH . C 3 HOH A 81 428 428 HOH HOH . C 3 HOH A 82 429 429 HOH HOH . C 3 HOH A 83 430 430 HOH HOH . C 3 HOH A 84 431 431 HOH HOH . C 3 HOH A 85 432 432 HOH HOH . C 3 HOH A 86 433 433 HOH HOH . C 3 HOH A 87 434 434 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 P1 A3P . . . B 2 -4.202 12.73 54.03 1 42.76 ? P1 A3P 347 A 1 HETATM 2 O O1P A3P . . . B 2 -4.235 11.279 54.504 1 41.71 ? O1P A3P 347 A 1 HETATM 3 O O2P A3P . . . B 2 -3.651 12.869 52.625 1 41.46 ? O2P A3P 347 A 1 HETATM 4 O O3P A3P . . . B 2 -5.521 13.456 54.226 1 41.16 ? O3P A3P 347 A 1 HETATM 5 P P2 A3P . . . B 2 -2.065 18.517 57.535 1 32.41 ? P2 A3P 347 A 1 HETATM 6 O O4P A3P . . . B 2 -0.692 19.135 57.677 1 35.45 ? O4P A3P 347 A 1 HETATM 7 O O5P A3P . . . B 2 -2.867 18.524 58.823 1 32.7 ? O5P A3P 347 A 1 HETATM 8 O O6P A3P . . . B 2 -2.844 19.09 56.364 1 34.26 ? O6P A3P 347 A 1 HETATM 9 O O5' A3P . . . B 2 -1.807 16.946 57.184 1 35.6 ? O5' A3P 347 A 1 HETATM 10 C C5' A3P . . . B 2 -2.917 16.041 57.011 1 35.52 ? C5' A3P 347 A 1 HETATM 11 C C4' A3P . . . B 2 -2.423 14.614 56.965 1 36.92 ? C4' A3P 347 A 1 HETATM 12 O O4' A3P . . . B 2 -2.201 14.124 58.299 1 35.69 ? O4' A3P 347 A 1 HETATM 13 C C3' A3P . . . B 2 -3.388 13.591 56.373 1 37.6 ? C3' A3P 347 A 1 HETATM 14 O O3' A3P . . . B 2 -3.14 13.479 54.975 1 40.49 ? O3' A3P 347 A 1 HETATM 15 C C2' A3P . . . B 2 -3.063 12.28 57.115 1 37.06 ? C2' A3P 347 A 1 HETATM 16 O O2' A3P . . . B 2 -2.427 11.329 56.28 1 36.61 ? O2' A3P 347 A 1 HETATM 17 C C1' A3P . . . B 2 -2.098 12.728 58.225 1 37.06 ? C1' A3P 347 A 1 HETATM 18 N N9 A3P . . . B 2 -2.336 12.166 59.558 1 36.04 ? N9 A3P 347 A 1 HETATM 19 C C8 A3P . . . B 2 -1.382 11.788 60.476 1 35.99 ? C8 A3P 347 A 1 HETATM 20 N N7 A3P . . . B 2 -1.879 11.323 61.597 1 34.98 ? N7 A3P 347 A 1 HETATM 21 C C5 A3P . . . B 2 -3.253 11.397 61.409 1 35.66 ? C5 A3P 347 A 1 HETATM 22 C C6 A3P . . . B 2 -4.339 11.129 62.265 1 36.46 ? C6 A3P 347 A 1 HETATM 23 N N6 A3P . . . B 2 -4.204 10.631 63.497 1 36.33 ? N6 A3P 347 A 1 HETATM 24 N N1 A3P . . . B 2 -5.583 11.394 61.805 1 37.77 ? N1 A3P 347 A 1 HETATM 25 C C2 A3P . . . B 2 -5.718 11.892 60.565 1 38.01 ? C2 A3P 347 A 1 HETATM 26 N N3 A3P . . . B 2 -4.776 12.181 59.665 1 38.51 ? N3 A3P 347 A 1 HETATM 27 C C4 A3P . . . B 2 -3.55 11.911 60.155 1 36.66 ? C4 A3P 347 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #