data_6B54 # _model_server_result.job_id Y3dSo9VVCN0r3Rp0bGvilA _model_server_result.datetime_utc '2024-11-26 01:43:27' _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 6b54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6B54 # _exptl.entry_id 6B54 _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 6B54 _cell.length_a 52.307 _cell.length_b 73.142 _cell.length_c 138.871 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 '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 6B54 _atom_sites.fract_transf_matrix[1][1] 0.019118 _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] 0.013672 _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] 0.007201 _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 93 HOH HOH . D 4 HOH A 2 402 53 HOH HOH . D 4 HOH A 3 403 171 HOH HOH . D 4 HOH A 4 404 86 HOH HOH . D 4 HOH A 5 405 77 HOH HOH . D 4 HOH A 6 406 51 HOH HOH . D 4 HOH A 7 407 185 HOH HOH . D 4 HOH A 8 408 158 HOH HOH . D 4 HOH A 9 409 141 HOH HOH . D 4 HOH A 10 410 134 HOH HOH . D 4 HOH A 11 411 68 HOH HOH . D 4 HOH A 12 412 75 HOH HOH . D 4 HOH A 13 413 90 HOH HOH . D 4 HOH A 14 414 82 HOH HOH . D 4 HOH A 15 415 78 HOH HOH . D 4 HOH A 16 416 59 HOH HOH . D 4 HOH A 17 417 115 HOH HOH . D 4 HOH A 18 418 31 HOH HOH . D 4 HOH A 19 419 190 HOH HOH . D 4 HOH A 20 420 105 HOH HOH . D 4 HOH A 21 421 91 HOH HOH . D 4 HOH A 22 422 148 HOH HOH . D 4 HOH A 23 423 72 HOH HOH . D 4 HOH A 24 424 102 HOH HOH . D 4 HOH A 25 425 21 HOH HOH . D 4 HOH A 26 426 219 HOH HOH . D 4 HOH A 27 427 35 HOH HOH . D 4 HOH A 28 428 145 HOH HOH . D 4 HOH A 29 429 16 HOH HOH . D 4 HOH A 30 430 166 HOH HOH . D 4 HOH A 31 431 64 HOH HOH . D 4 HOH A 32 432 44 HOH HOH . D 4 HOH A 33 433 146 HOH HOH . D 4 HOH A 34 434 74 HOH HOH . D 4 HOH A 35 435 159 HOH HOH . D 4 HOH A 36 436 4 HOH HOH . D 4 HOH A 37 437 223 HOH HOH . D 4 HOH A 38 438 164 HOH HOH . D 4 HOH A 39 439 167 HOH HOH . D 4 HOH A 40 440 117 HOH HOH . D 4 HOH A 41 441 124 HOH HOH . D 4 HOH A 42 442 119 HOH HOH . D 4 HOH A 43 443 49 HOH HOH . D 4 HOH A 44 444 14 HOH HOH . D 4 HOH A 45 445 62 HOH HOH . D 4 HOH A 46 446 55 HOH HOH . D 4 HOH A 47 447 43 HOH HOH . D 4 HOH A 48 448 12 HOH HOH . D 4 HOH A 49 449 65 HOH HOH . D 4 HOH A 50 450 20 HOH HOH . D 4 HOH A 51 451 99 HOH HOH . D 4 HOH A 52 452 19 HOH HOH . D 4 HOH A 53 453 71 HOH HOH . D 4 HOH A 54 454 28 HOH HOH . D 4 HOH A 55 455 131 HOH HOH . D 4 HOH A 56 456 52 HOH HOH . D 4 HOH A 57 457 15 HOH HOH . D 4 HOH A 58 458 11 HOH HOH . D 4 HOH A 59 459 39 HOH HOH . D 4 HOH A 60 460 33 HOH HOH . D 4 HOH A 61 461 2 HOH HOH . D 4 HOH A 62 462 13 HOH HOH . D 4 HOH A 63 463 94 HOH HOH . D 4 HOH A 64 464 111 HOH HOH . D 4 HOH A 65 465 9 HOH HOH . D 4 HOH A 66 466 160 HOH HOH . D 4 HOH A 67 467 8 HOH HOH . D 4 HOH A 68 468 27 HOH HOH . D 4 HOH A 69 469 122 HOH HOH . D 4 HOH A 70 470 142 HOH HOH . D 4 HOH A 71 471 118 HOH HOH . D 4 HOH A 72 472 121 HOH HOH . D 4 HOH A 73 473 149 HOH HOH . D 4 HOH A 74 474 193 HOH HOH . D 4 HOH A 75 475 106 HOH HOH . D 4 HOH A 76 476 69 HOH HOH . D 4 HOH A 77 477 89 HOH HOH . D 4 HOH A 78 478 45 HOH HOH . D 4 HOH A 79 479 139 HOH HOH . D 4 HOH A 80 480 36 HOH HOH . D 4 HOH A 81 481 6 HOH HOH . D 4 HOH A 82 482 61 HOH HOH . D 4 HOH A 83 483 38 HOH HOH . D 4 HOH A 84 484 92 HOH HOH . D 4 HOH A 85 485 30 HOH HOH . D 4 HOH A 86 486 178 HOH HOH . D 4 HOH A 87 487 29 HOH HOH . D 4 HOH A 88 488 1 HOH HOH . D 4 HOH A 89 489 67 HOH HOH . D 4 HOH A 90 490 70 HOH HOH . D 4 HOH A 91 491 116 HOH HOH . D 4 HOH A 92 492 175 HOH HOH . D 4 HOH A 93 493 42 HOH HOH . D 4 HOH A 94 494 3 HOH HOH . D 4 HOH A 95 495 23 HOH HOH . D 4 HOH A 96 496 143 HOH HOH . D 4 HOH A 97 497 132 HOH HOH . D 4 HOH A 98 498 41 HOH HOH . D 4 HOH A 99 499 25 HOH HOH . D 4 HOH A 100 500 100 HOH HOH . D 4 HOH A 101 501 103 HOH HOH . D 4 HOH A 102 502 5 HOH HOH . D 4 HOH A 103 503 109 HOH HOH . D 4 HOH A 104 504 209 HOH HOH . D 4 HOH A 105 505 180 HOH HOH . D 4 HOH A 106 506 112 HOH HOH . D 4 HOH A 107 507 225 HOH HOH . D 4 HOH A 108 508 79 HOH HOH . D 4 HOH A 109 509 214 HOH HOH . D 4 HOH A 110 510 130 HOH HOH . D 4 HOH A 111 511 161 HOH HOH . D 4 HOH A 112 512 60 HOH HOH . D 4 HOH A 113 513 24 HOH HOH . D 4 HOH A 114 514 22 HOH HOH . D 4 HOH A 115 515 58 HOH HOH . D 4 HOH A 116 516 85 HOH HOH . D 4 HOH A 117 517 46 HOH HOH . D 4 HOH A 118 518 83 HOH HOH . D 4 HOH A 119 519 84 HOH HOH . D 4 HOH A 120 520 168 HOH HOH . D 4 HOH A 121 521 97 HOH HOH . D 4 HOH A 122 522 7 HOH HOH . D 4 HOH A 123 523 101 HOH HOH . D 4 HOH A 124 524 48 HOH HOH . D 4 HOH A 125 525 210 HOH HOH . D 4 HOH A 126 526 217 HOH HOH . D 4 HOH A 127 527 76 HOH HOH . D 4 HOH A 128 528 182 HOH HOH . D 4 HOH A 129 529 194 HOH HOH . D 4 HOH A 130 530 128 HOH HOH . D 4 HOH A 131 531 220 HOH HOH . D 4 HOH A 132 532 216 HOH HOH . D 4 HOH A 133 533 203 HOH HOH . D 4 HOH A 134 534 222 HOH HOH . D 4 HOH A 135 535 34 HOH HOH . D 4 HOH A 136 536 202 HOH HOH . D 4 HOH A 137 537 169 HOH HOH . D 4 HOH A 138 538 123 HOH HOH . D 4 HOH A 139 539 212 HOH HOH . D 4 HOH A 140 540 10 HOH HOH . D 4 HOH A 141 541 137 HOH HOH . D 4 HOH A 142 542 26 HOH HOH . D 4 HOH A 143 543 165 HOH HOH . D 4 HOH A 144 544 66 HOH HOH . D 4 HOH A 145 545 63 HOH HOH . D 4 HOH A 146 546 80 HOH HOH . D 4 HOH A 147 547 211 HOH HOH . D 4 HOH A 148 548 54 HOH HOH . D 4 HOH A 149 549 47 HOH HOH . D 4 HOH A 150 550 205 HOH HOH . D 4 HOH A 151 551 73 HOH HOH . D 4 HOH A 152 552 188 HOH HOH . D 4 HOH A 153 553 87 HOH HOH . D 4 HOH A 154 554 113 HOH HOH . D 4 HOH A 155 555 173 HOH HOH . D 4 HOH A 156 556 17 HOH HOH . D 4 HOH A 157 557 136 HOH HOH . D 4 HOH A 158 558 140 HOH HOH . D 4 HOH A 159 559 110 HOH HOH . D 4 HOH A 160 560 108 HOH HOH . D 4 HOH A 161 561 186 HOH HOH . D 4 HOH A 162 562 126 HOH HOH . D 4 HOH A 163 563 107 HOH HOH . D 4 HOH A 164 564 135 HOH HOH . D 4 HOH A 165 565 150 HOH HOH . D 4 HOH A 166 566 174 HOH HOH . D 4 HOH A 167 567 114 HOH HOH . D 4 HOH A 168 568 18 HOH HOH . D 4 HOH A 169 569 206 HOH HOH . D 4 HOH A 170 570 138 HOH HOH . D 4 HOH A 171 571 183 HOH HOH . D 4 HOH A 172 572 57 HOH HOH . D 4 HOH A 173 573 200 HOH HOH . D 4 HOH A 174 574 154 HOH HOH . D 4 HOH A 175 575 81 HOH HOH . D 4 HOH A 176 576 162 HOH HOH . D 4 HOH A 177 577 32 HOH HOH . D 4 HOH A 178 578 37 HOH HOH . D 4 HOH A 179 579 218 HOH HOH . D 4 HOH A 180 580 172 HOH HOH . D 4 HOH A 181 581 157 HOH HOH . D 4 HOH A 182 582 201 HOH HOH . D 4 HOH A 183 583 152 HOH HOH . D 4 HOH A 184 584 199 HOH HOH . D 4 HOH A 185 585 189 HOH HOH . D 4 HOH A 186 586 176 HOH HOH . D 4 HOH A 187 587 129 HOH HOH . D 4 HOH A 188 588 144 HOH HOH . D 4 HOH A 189 589 192 HOH HOH . D 4 HOH A 190 590 196 HOH HOH . D 4 HOH A 191 591 224 HOH HOH . D 4 HOH A 192 592 40 HOH HOH . D 4 HOH A 193 593 98 HOH HOH . D 4 HOH A 194 594 197 HOH HOH . D 4 HOH A 195 595 151 HOH HOH . D 4 HOH A 196 596 179 HOH HOH . D 4 HOH A 197 597 181 HOH HOH . D 4 HOH A 198 598 153 HOH HOH . D 4 HOH A 199 599 88 HOH HOH . D 4 HOH A 200 600 177 HOH HOH . D 4 HOH A 201 601 221 HOH HOH . D 4 HOH A 202 602 191 HOH HOH . D 4 HOH A 203 603 127 HOH HOH . D 4 HOH A 204 604 204 HOH HOH . D 4 HOH A 205 605 163 HOH HOH . D 4 HOH A 206 606 208 HOH HOH . D 4 HOH A 207 607 50 HOH HOH . D 4 HOH A 208 608 133 HOH HOH . D 4 HOH A 209 609 120 HOH HOH . D 4 HOH A 210 610 125 HOH HOH . D 4 HOH A 211 611 96 HOH HOH . D 4 HOH A 212 612 187 HOH HOH . D 4 HOH A 213 613 95 HOH HOH . D 4 HOH A 214 614 184 HOH HOH . D 4 HOH A 215 615 198 HOH HOH . D 4 HOH A 216 616 104 HOH HOH . D 4 HOH A 217 617 147 HOH HOH . D 4 HOH A 218 618 56 HOH HOH . D 4 HOH A 219 619 215 HOH HOH . D 4 HOH A 220 620 170 HOH HOH . D 4 HOH A 221 621 207 HOH HOH . D 4 HOH A 222 622 156 HOH HOH . D 4 HOH A 223 623 195 HOH HOH . D 4 HOH A 224 624 155 HOH HOH . D 4 HOH A 225 625 213 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 -6.808 -3.173 -16.947 1 20.88 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 -7.432 -2.55 -18.172 1 24.56 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 -6.732 -2.196 -15.795 1 21.65 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 -7.585 -4.389 -16.506 1 19.77 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 -2.682 -8.98 -18.344 1 19.46 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 -2.606 -9.234 -19.85 1 17.39 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 -1.48 -9.48 -17.587 1 21.18 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 -3.991 -9.592 -17.862 1 21.9 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 -2.686 -7.39 -18.167 1 20.9 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 -3.885 -6.697 -18.559 1 18.22 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 -3.822 -5.276 -18.055 1 20.76 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 -2.714 -4.522 -18.636 1 22.62 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 -5.048 -4.483 -18.402 1 21.67 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 -5.293 -3.562 -17.321 1 18.05 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 -4.646 -3.806 -19.655 1 25 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 -5.494 -2.711 -19.954 1 23.63 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 -3.248 -3.379 -19.332 1 21.44 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 -2.428 -3.13 -20.466 1 28 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 -1.999 -4.022 -21.382 1 27.73 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 -1.224 -3.402 -22.291 1 21.98 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 -1.147 -2.067 -21.955 1 26.53 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 -0.481 -0.912 -22.497 1 29.33 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 0.305 -1.007 -23.656 1 26.66 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 -0.63 0.277 -21.876 1 28.36 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 -1.369 0.396 -20.776 1 25.99 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 -1.991 -0.647 -20.225 1 26.15 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 -1.905 -1.894 -20.781 1 25.14 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #