data_5BYJ # _model_server_result.job_id zfso1Tlg7FOiHswyOHZD3Q _model_server_result.datetime_utc '2024-12-01 18:30:10' _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 5byj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5BYJ # _exptl.entry_id 5BYJ _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 5BYJ _cell.length_a 140.542 _cell.length_b 39.237 _cell.length_c 54.009 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BYJ _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 1 281.084 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 5BYJ _atom_sites.fract_transf_matrix[1][1] 0.007115 _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] 0.025486 _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] 0.018515 _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 OQR A 1 302 401 OQR OQR . D 4 HOH A 1 401 118 HOH HOH . D 4 HOH A 2 402 65 HOH HOH . D 4 HOH A 3 403 139 HOH HOH . D 4 HOH A 4 404 38 HOH HOH . D 4 HOH A 5 405 206 HOH HOH . D 4 HOH A 6 406 90 HOH HOH . D 4 HOH A 7 407 204 HOH HOH . D 4 HOH A 8 408 148 HOH HOH . D 4 HOH A 9 409 78 HOH HOH . D 4 HOH A 10 410 29 HOH HOH . D 4 HOH A 11 411 199 HOH HOH . D 4 HOH A 12 412 180 HOH HOH . D 4 HOH A 13 413 201 HOH HOH . D 4 HOH A 14 414 41 HOH HOH . D 4 HOH A 15 415 36 HOH HOH . D 4 HOH A 16 416 157 HOH HOH . D 4 HOH A 17 417 190 HOH HOH . D 4 HOH A 18 418 85 HOH HOH . D 4 HOH A 19 419 79 HOH HOH . D 4 HOH A 20 420 26 HOH HOH . D 4 HOH A 21 421 196 HOH HOH . D 4 HOH A 22 422 149 HOH HOH . D 4 HOH A 23 423 174 HOH HOH . D 4 HOH A 24 424 211 HOH HOH . D 4 HOH A 25 425 100 HOH HOH . D 4 HOH A 26 426 19 HOH HOH . D 4 HOH A 27 427 58 HOH HOH . D 4 HOH A 28 428 151 HOH HOH . D 4 HOH A 29 429 177 HOH HOH . D 4 HOH A 30 430 188 HOH HOH . D 4 HOH A 31 431 213 HOH HOH . D 4 HOH A 32 432 200 HOH HOH . D 4 HOH A 33 433 207 HOH HOH . D 4 HOH A 34 434 2 HOH HOH . D 4 HOH A 35 435 24 HOH HOH . D 4 HOH A 36 436 18 HOH HOH . D 4 HOH A 37 437 12 HOH HOH . D 4 HOH A 38 438 96 HOH HOH . D 4 HOH A 39 439 22 HOH HOH . D 4 HOH A 40 440 155 HOH HOH . D 4 HOH A 41 441 141 HOH HOH . D 4 HOH A 42 442 171 HOH HOH . D 4 HOH A 43 443 129 HOH HOH . D 4 HOH A 44 444 40 HOH HOH . D 4 HOH A 45 445 55 HOH HOH . D 4 HOH A 46 446 39 HOH HOH . D 4 HOH A 47 447 33 HOH HOH . D 4 HOH A 48 448 57 HOH HOH . D 4 HOH A 49 449 54 HOH HOH . D 4 HOH A 50 450 76 HOH HOH . D 4 HOH A 51 451 59 HOH HOH . D 4 HOH A 52 452 184 HOH HOH . D 4 HOH A 53 453 193 HOH HOH . D 4 HOH A 54 454 133 HOH HOH . D 4 HOH A 55 455 156 HOH HOH . D 4 HOH A 56 456 163 HOH HOH . D 4 HOH A 57 457 102 HOH HOH . D 4 HOH A 58 458 53 HOH HOH . D 4 HOH A 59 459 160 HOH HOH . D 4 HOH A 60 460 83 HOH HOH . D 4 HOH A 61 461 28 HOH HOH . D 4 HOH A 62 462 111 HOH HOH . D 4 HOH A 63 463 14 HOH HOH . D 4 HOH A 64 464 27 HOH HOH . D 4 HOH A 65 465 127 HOH HOH . D 4 HOH A 66 466 108 HOH HOH . D 4 HOH A 67 467 117 HOH HOH . D 4 HOH A 68 468 77 HOH HOH . D 4 HOH A 69 469 5 HOH HOH . D 4 HOH A 70 470 86 HOH HOH . D 4 HOH A 71 471 43 HOH HOH . D 4 HOH A 72 472 10 HOH HOH . D 4 HOH A 73 473 136 HOH HOH . D 4 HOH A 74 474 179 HOH HOH . D 4 HOH A 75 475 70 HOH HOH . D 4 HOH A 76 476 164 HOH HOH . D 4 HOH A 77 477 168 HOH HOH . D 4 HOH A 78 478 167 HOH HOH . D 4 HOH A 79 479 176 HOH HOH . D 4 HOH A 80 480 98 HOH HOH . D 4 HOH A 81 481 23 HOH HOH . D 4 HOH A 82 482 3 HOH HOH . D 4 HOH A 83 483 1 HOH HOH . D 4 HOH A 84 484 51 HOH HOH . D 4 HOH A 85 485 150 HOH HOH . D 4 HOH A 86 486 92 HOH HOH . D 4 HOH A 87 487 116 HOH HOH . D 4 HOH A 88 488 124 HOH HOH . D 4 HOH A 89 489 73 HOH HOH . D 4 HOH A 90 490 121 HOH HOH . D 4 HOH A 91 491 68 HOH HOH . D 4 HOH A 92 492 60 HOH HOH . D 4 HOH A 93 493 6 HOH HOH . D 4 HOH A 94 494 34 HOH HOH . D 4 HOH A 95 495 88 HOH HOH . D 4 HOH A 96 496 20 HOH HOH . D 4 HOH A 97 497 158 HOH HOH . D 4 HOH A 98 498 120 HOH HOH . D 4 HOH A 99 499 37 HOH HOH . D 4 HOH A 100 500 138 HOH HOH . D 4 HOH A 101 501 8 HOH HOH . D 4 HOH A 102 502 71 HOH HOH . D 4 HOH A 103 503 9 HOH HOH . D 4 HOH A 104 504 17 HOH HOH . D 4 HOH A 105 505 16 HOH HOH . D 4 HOH A 106 506 99 HOH HOH . D 4 HOH A 107 507 21 HOH HOH . D 4 HOH A 108 508 192 HOH HOH . D 4 HOH A 109 509 48 HOH HOH . D 4 HOH A 110 510 46 HOH HOH . D 4 HOH A 111 511 146 HOH HOH . D 4 HOH A 112 512 47 HOH HOH . D 4 HOH A 113 513 56 HOH HOH . D 4 HOH A 114 514 162 HOH HOH . D 4 HOH A 115 515 183 HOH HOH . D 4 HOH A 116 516 97 HOH HOH . D 4 HOH A 117 517 4 HOH HOH . D 4 HOH A 118 518 45 HOH HOH . D 4 HOH A 119 519 209 HOH HOH . D 4 HOH A 120 520 49 HOH HOH . D 4 HOH A 121 521 178 HOH HOH . D 4 HOH A 122 522 205 HOH HOH . D 4 HOH A 123 523 112 HOH HOH . D 4 HOH A 124 524 63 HOH HOH . D 4 HOH A 125 525 109 HOH HOH . D 4 HOH A 126 526 35 HOH HOH . D 4 HOH A 127 527 169 HOH HOH . D 4 HOH A 128 528 195 HOH HOH . D 4 HOH A 129 529 42 HOH HOH . D 4 HOH A 130 530 66 HOH HOH . D 4 HOH A 131 531 13 HOH HOH . D 4 HOH A 132 532 62 HOH HOH . D 4 HOH A 133 533 101 HOH HOH . D 4 HOH A 134 534 75 HOH HOH . D 4 HOH A 135 535 61 HOH HOH . D 4 HOH A 136 536 32 HOH HOH . D 4 HOH A 137 537 80 HOH HOH . D 4 HOH A 138 538 25 HOH HOH . D 4 HOH A 139 539 137 HOH HOH . D 4 HOH A 140 540 11 HOH HOH . D 4 HOH A 141 541 107 HOH HOH . D 4 HOH A 142 542 132 HOH HOH . D 4 HOH A 143 543 210 HOH HOH . D 4 HOH A 144 544 104 HOH HOH . D 4 HOH A 145 545 93 HOH HOH . D 4 HOH A 146 546 7 HOH HOH . D 4 HOH A 147 547 64 HOH HOH . D 4 HOH A 148 548 91 HOH HOH . D 4 HOH A 149 549 125 HOH HOH . D 4 HOH A 150 550 69 HOH HOH . D 4 HOH A 151 551 114 HOH HOH . D 4 HOH A 152 552 67 HOH HOH . D 4 HOH A 153 553 215 HOH HOH . D 4 HOH A 154 554 52 HOH HOH . D 4 HOH A 155 555 82 HOH HOH . D 4 HOH A 156 556 166 HOH HOH . D 4 HOH A 157 557 170 HOH HOH . D 4 HOH A 158 558 31 HOH HOH . D 4 HOH A 159 559 161 HOH HOH . D 4 HOH A 160 560 74 HOH HOH . D 4 HOH A 161 561 89 HOH HOH . D 4 HOH A 162 562 186 HOH HOH . D 4 HOH A 163 563 44 HOH HOH . D 4 HOH A 164 564 173 HOH HOH . D 4 HOH A 165 565 106 HOH HOH . D 4 HOH A 166 566 172 HOH HOH . D 4 HOH A 167 567 143 HOH HOH . D 4 HOH A 168 568 128 HOH HOH . D 4 HOH A 169 569 30 HOH HOH . D 4 HOH A 170 570 122 HOH HOH . D 4 HOH A 171 571 72 HOH HOH . D 4 HOH A 172 572 115 HOH HOH . D 4 HOH A 173 573 15 HOH HOH . D 4 HOH A 174 574 87 HOH HOH . D 4 HOH A 175 575 110 HOH HOH . D 4 HOH A 176 576 50 HOH HOH . D 4 HOH A 177 577 153 HOH HOH . D 4 HOH A 178 578 154 HOH HOH . D 4 HOH A 179 579 145 HOH HOH . D 4 HOH A 180 580 103 HOH HOH . D 4 HOH A 181 581 212 HOH HOH . D 4 HOH A 182 582 203 HOH HOH . D 4 HOH A 183 583 217 HOH HOH . D 4 HOH A 184 584 197 HOH HOH . D 4 HOH A 185 585 81 HOH HOH . D 4 HOH A 186 586 152 HOH HOH . D 4 HOH A 187 587 119 HOH HOH . D 4 HOH A 188 588 214 HOH HOH . D 4 HOH A 189 589 198 HOH HOH . D 4 HOH A 190 590 182 HOH HOH . D 4 HOH A 191 591 123 HOH HOH . D 4 HOH A 192 592 181 HOH HOH . D 4 HOH A 193 593 175 HOH HOH . D 4 HOH A 194 594 140 HOH HOH . D 4 HOH A 195 595 187 HOH HOH . D 4 HOH A 196 596 144 HOH HOH . D 4 HOH A 197 597 130 HOH HOH . D 4 HOH A 198 598 95 HOH HOH . D 4 HOH A 199 599 189 HOH HOH . D 4 HOH A 200 600 191 HOH HOH . D 4 HOH A 201 601 134 HOH HOH . D 4 HOH A 202 602 105 HOH HOH . D 4 HOH A 203 603 126 HOH HOH . D 4 HOH A 204 604 202 HOH HOH . D 4 HOH A 205 605 194 HOH HOH . D 4 HOH A 206 606 142 HOH HOH . D 4 HOH A 207 607 165 HOH HOH . D 4 HOH A 208 608 216 HOH HOH . D 4 HOH A 209 609 147 HOH HOH . D 4 HOH A 210 610 185 HOH HOH . D 4 HOH A 211 611 159 HOH HOH . D 4 HOH A 212 612 131 HOH HOH . D 4 HOH A 213 613 208 HOH HOH . D 4 HOH A 214 614 94 HOH HOH . D 4 HOH A 215 615 113 HOH HOH . D 4 HOH A 216 616 135 HOH HOH . D 4 HOH A 217 617 84 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 2 110.438 -4.286 13.834 1 24.44 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 110.052 -5.129 12.64 1 24.43 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 109.751 -2.927 13.815 1 24.66 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 110.133 -4.977 15.136 1 23.52 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 115.678 0.765 14.346 1 21.62 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 116.691 1.021 13.26 1 21.34 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 116.278 0.789 15.72 1 20.78 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 114.473 1.673 14.234 1 21.28 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 115.242 -0.736 14.025 1 25.91 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 114.292 -1.423 14.846 1 21.18 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 113.905 -2.699 14.155 1 20.39 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 114.999 -3.66 14.222 1 20.52 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 112.741 -3.369 14.815 1 20.3 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 112.041 -4.117 13.802 1 23.36 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 113.408 -4.278 15.782 1 20.69 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 112.555 -5.339 16.201 1 22.78 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 114.554 -4.806 14.982 1 21.88 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 115.641 -5.271 15.764 1 20.46 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 116.409 -4.516 16.549 1 25.24 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 117.341 -5.27 17.137 1 22.99 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 117.173 -6.559 16.707 1 25.56 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 117.843 -7.799 16.959 1 30.94 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 118.94 -7.861 17.834 1 23.61 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 117.393 -8.906 16.349 1 26.99 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 116.355 -8.861 15.524 1 25.6 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 115.702 -7.73 15.258 1 24.3 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 116.077 -6.557 15.833 1 22.89 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #