data_6B50 # _model_server_result.job_id Or_a7ktFpdqNU9ziAf723w _model_server_result.datetime_utc '2025-02-18 18:26:29' _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 6b50 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6B50 # _exptl.entry_id 6B50 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _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 6B50 _cell.length_a 140.188 _cell.length_b 39.401 _cell.length_c 53.816 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B50 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 280.376 0 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 '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 6B50 _atom_sites.fract_transf_matrix[1][1] 0.007133 _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] 0.02538 _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] 0.018582 _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 1 301 301 A3P A3P . C 3 OAQ A 1 302 401 OAQ OAQ . D 4 HOH A 1 401 50 HOH HOH . D 4 HOH A 2 402 126 HOH HOH . D 4 HOH A 3 403 97 HOH HOH . D 4 HOH A 4 404 84 HOH HOH . D 4 HOH A 5 405 102 HOH HOH . D 4 HOH A 6 406 77 HOH HOH . D 4 HOH A 7 407 116 HOH HOH . D 4 HOH A 8 408 90 HOH HOH . D 4 HOH A 9 409 87 HOH HOH . D 4 HOH A 10 410 51 HOH HOH . D 4 HOH A 11 411 80 HOH HOH . D 4 HOH A 12 412 29 HOH HOH . D 4 HOH A 13 413 96 HOH HOH . D 4 HOH A 14 414 59 HOH HOH . D 4 HOH A 15 415 55 HOH HOH . D 4 HOH A 16 416 92 HOH HOH . D 4 HOH A 17 417 2 HOH HOH . D 4 HOH A 18 418 94 HOH HOH . D 4 HOH A 19 419 6 HOH HOH . D 4 HOH A 20 420 43 HOH HOH . D 4 HOH A 21 421 27 HOH HOH . D 4 HOH A 22 422 73 HOH HOH . D 4 HOH A 23 423 109 HOH HOH . D 4 HOH A 24 424 49 HOH HOH . D 4 HOH A 25 425 93 HOH HOH . D 4 HOH A 26 426 10 HOH HOH . D 4 HOH A 27 427 121 HOH HOH . D 4 HOH A 28 428 35 HOH HOH . D 4 HOH A 29 429 81 HOH HOH . D 4 HOH A 30 430 23 HOH HOH . D 4 HOH A 31 431 53 HOH HOH . D 4 HOH A 32 432 18 HOH HOH . D 4 HOH A 33 433 125 HOH HOH . D 4 HOH A 34 434 17 HOH HOH . D 4 HOH A 35 435 57 HOH HOH . D 4 HOH A 36 436 26 HOH HOH . D 4 HOH A 37 437 16 HOH HOH . D 4 HOH A 38 438 101 HOH HOH . D 4 HOH A 39 439 42 HOH HOH . D 4 HOH A 40 440 11 HOH HOH . D 4 HOH A 41 441 37 HOH HOH . D 4 HOH A 42 442 63 HOH HOH . D 4 HOH A 43 443 100 HOH HOH . D 4 HOH A 44 444 98 HOH HOH . D 4 HOH A 45 445 99 HOH HOH . D 4 HOH A 46 446 3 HOH HOH . D 4 HOH A 47 447 5 HOH HOH . D 4 HOH A 48 448 60 HOH HOH . D 4 HOH A 49 449 108 HOH HOH . D 4 HOH A 50 450 40 HOH HOH . D 4 HOH A 51 451 21 HOH HOH . D 4 HOH A 52 452 15 HOH HOH . D 4 HOH A 53 453 36 HOH HOH . D 4 HOH A 54 454 39 HOH HOH . D 4 HOH A 55 455 4 HOH HOH . D 4 HOH A 56 456 32 HOH HOH . D 4 HOH A 57 457 46 HOH HOH . D 4 HOH A 58 458 25 HOH HOH . D 4 HOH A 59 459 30 HOH HOH . D 4 HOH A 60 460 78 HOH HOH . D 4 HOH A 61 461 54 HOH HOH . D 4 HOH A 62 462 56 HOH HOH . D 4 HOH A 63 463 86 HOH HOH . D 4 HOH A 64 464 8 HOH HOH . D 4 HOH A 65 465 65 HOH HOH . D 4 HOH A 66 466 47 HOH HOH . D 4 HOH A 67 467 38 HOH HOH . D 4 HOH A 68 468 117 HOH HOH . D 4 HOH A 69 469 13 HOH HOH . D 4 HOH A 70 470 7 HOH HOH . D 4 HOH A 71 471 41 HOH HOH . D 4 HOH A 72 472 113 HOH HOH . D 4 HOH A 73 473 1 HOH HOH . D 4 HOH A 74 474 64 HOH HOH . D 4 HOH A 75 475 9 HOH HOH . D 4 HOH A 76 476 66 HOH HOH . D 4 HOH A 77 477 128 HOH HOH . D 4 HOH A 78 478 68 HOH HOH . D 4 HOH A 79 479 19 HOH HOH . D 4 HOH A 80 480 48 HOH HOH . D 4 HOH A 81 481 20 HOH HOH . D 4 HOH A 82 482 61 HOH HOH . D 4 HOH A 83 483 14 HOH HOH . D 4 HOH A 84 484 71 HOH HOH . D 4 HOH A 85 485 112 HOH HOH . D 4 HOH A 86 486 62 HOH HOH . D 4 HOH A 87 487 130 HOH HOH . D 4 HOH A 88 488 34 HOH HOH . D 4 HOH A 89 489 75 HOH HOH . D 4 HOH A 90 490 33 HOH HOH . D 4 HOH A 91 491 28 HOH HOH . D 4 HOH A 92 492 89 HOH HOH . D 4 HOH A 93 493 83 HOH HOH . D 4 HOH A 94 494 31 HOH HOH . D 4 HOH A 95 495 115 HOH HOH . D 4 HOH A 96 496 76 HOH HOH . D 4 HOH A 97 497 52 HOH HOH . D 4 HOH A 98 498 122 HOH HOH . D 4 HOH A 99 499 44 HOH HOH . D 4 HOH A 100 500 91 HOH HOH . D 4 HOH A 101 501 12 HOH HOH . D 4 HOH A 102 502 70 HOH HOH . D 4 HOH A 103 503 124 HOH HOH . D 4 HOH A 104 504 74 HOH HOH . D 4 HOH A 105 505 24 HOH HOH . D 4 HOH A 106 506 114 HOH HOH . D 4 HOH A 107 507 111 HOH HOH . D 4 HOH A 108 508 22 HOH HOH . D 4 HOH A 109 509 105 HOH HOH . D 4 HOH A 110 510 118 HOH HOH . D 4 HOH A 111 511 120 HOH HOH . D 4 HOH A 112 512 119 HOH HOH . D 4 HOH A 113 513 79 HOH HOH . D 4 HOH A 114 514 85 HOH HOH . D 4 HOH A 115 515 72 HOH HOH . D 4 HOH A 116 516 88 HOH HOH . D 4 HOH A 117 517 45 HOH HOH . D 4 HOH A 118 518 104 HOH HOH . D 4 HOH A 119 519 95 HOH HOH . D 4 HOH A 120 520 110 HOH HOH . D 4 HOH A 121 521 58 HOH HOH . D 4 HOH A 122 522 106 HOH HOH . D 4 HOH A 123 523 127 HOH HOH . D 4 HOH A 124 524 67 HOH HOH . D 4 HOH A 125 525 107 HOH HOH . D 4 HOH A 126 526 123 HOH HOH . D 4 HOH A 127 527 82 HOH HOH . D 4 HOH A 128 528 103 HOH HOH . D 4 HOH A 129 529 69 HOH HOH . D 4 HOH A 130 530 129 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 2 110.083 -4.282 13.86 1 18.52 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 109.757 -5.032 12.598 1 18.52 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 109.349 -2.962 13.888 1 18.27 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 109.756 -5.039 15.119 1 21.76 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 115.366 0.81 14.237 1 17.43 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 116.374 1.129 13.17 1 14.79 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 115.91 0.919 15.63 1 13.83 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 114.07 1.631 14.094 1 14.9 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 114.99 -0.724 13.971 1 18.31 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 113.952 -1.347 14.736 1 14.67 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 113.574 -2.65 14.082 1 14.26 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 114.667 -3.608 14.169 1 18.74 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 112.398 -3.312 14.751 1 13.49 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 111.694 -4.076 13.783 1 13.92 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 113.039 -4.221 15.732 1 17.6 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 112.196 -5.292 16.111 1 19.18 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 114.212 -4.724 14.964 1 16.19 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 115.271 -5.173 15.779 1 19.96 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 116.035 -4.42 16.569 1 22.96 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 116.948 -5.185 17.186 1 22.22 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 116.785 -6.476 16.772 1 21.94 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 117.439 -7.713 17.066 1 24.53 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 118.524 -7.776 17.963 1 23.34 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 116.995 -8.821 16.456 1 22.95 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 115.976 -8.777 15.602 1 23.86 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 115.334 -7.645 15.301 1 21.26 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 115.704 -6.469 15.865 1 19.21 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #