data_3JXU # _model_server_result.job_id hN8BEvSqxngttkE_xYwrPg _model_server_result.datetime_utc '2024-11-22 00:14:12' _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 3jxu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":486}' # _entry.id 3JXU # _exptl.entry_id 3JXU _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-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 3JXU _cell.length_a 46.013 _cell.length_b 63.298 _cell.length_c 144.197 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JXU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,E _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 metalc ? metalc1 B O2B ADP . A ADP 486 1_555 C MG MG . A MG 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc2 C MG MG . A MG 487 1_555 D O2 PO4 . A PO4 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc3 C MG MG . A MG 487 1_555 E O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 C MG MG . A MG 487 1_555 E O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc5 C MG MG . A MG 487 1_555 E O HOH . A HOH 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc6 C MG MG . A MG 487 1_555 E O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3JXU _atom_sites.fract_transf_matrix[1][1] 0.021733 _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] 0.015798 _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] 0.006935 _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 ADP A 1 486 486 ADP ADP . C 3 MG A 1 487 487 MG MG . D 4 PO4 A 1 488 488 PO4 PO4 . E 5 HOH A 1 388 4 HOH HOH . E 5 HOH A 2 389 5 HOH HOH . E 5 HOH A 3 390 6 HOH HOH . E 5 HOH A 4 391 7 HOH HOH . E 5 HOH A 5 392 8 HOH HOH . E 5 HOH A 6 393 9 HOH HOH . E 5 HOH A 7 394 10 HOH HOH . E 5 HOH A 8 395 11 HOH HOH . E 5 HOH A 9 396 12 HOH HOH . E 5 HOH A 10 397 13 HOH HOH . E 5 HOH A 11 398 14 HOH HOH . E 5 HOH A 12 399 15 HOH HOH . E 5 HOH A 13 400 16 HOH HOH . E 5 HOH A 14 401 17 HOH HOH . E 5 HOH A 15 402 18 HOH HOH . E 5 HOH A 16 403 19 HOH HOH . E 5 HOH A 17 404 20 HOH HOH . E 5 HOH A 18 405 21 HOH HOH . E 5 HOH A 19 406 22 HOH HOH . E 5 HOH A 20 407 23 HOH HOH . E 5 HOH A 21 408 24 HOH HOH . E 5 HOH A 22 409 25 HOH HOH . E 5 HOH A 23 410 26 HOH HOH . E 5 HOH A 24 411 27 HOH HOH . E 5 HOH A 25 412 28 HOH HOH . E 5 HOH A 26 413 29 HOH HOH . E 5 HOH A 27 414 30 HOH HOH . E 5 HOH A 28 415 31 HOH HOH . E 5 HOH A 29 416 32 HOH HOH . E 5 HOH A 30 417 33 HOH HOH . E 5 HOH A 31 418 34 HOH HOH . E 5 HOH A 32 419 35 HOH HOH . E 5 HOH A 33 420 36 HOH HOH . E 5 HOH A 34 421 37 HOH HOH . E 5 HOH A 35 422 38 HOH HOH . E 5 HOH A 36 423 39 HOH HOH . E 5 HOH A 37 424 40 HOH HOH . E 5 HOH A 38 425 42 HOH HOH . E 5 HOH A 39 426 43 HOH HOH . E 5 HOH A 40 427 44 HOH HOH . E 5 HOH A 41 428 45 HOH HOH . E 5 HOH A 42 429 46 HOH HOH . E 5 HOH A 43 430 48 HOH HOH . E 5 HOH A 44 431 49 HOH HOH . E 5 HOH A 45 432 50 HOH HOH . E 5 HOH A 46 433 51 HOH HOH . E 5 HOH A 47 434 53 HOH HOH . E 5 HOH A 48 435 54 HOH HOH . E 5 HOH A 49 436 55 HOH HOH . E 5 HOH A 50 437 56 HOH HOH . E 5 HOH A 51 438 57 HOH HOH . E 5 HOH A 52 439 58 HOH HOH . E 5 HOH A 53 440 59 HOH HOH . E 5 HOH A 54 441 60 HOH HOH . E 5 HOH A 55 442 61 HOH HOH . E 5 HOH A 56 443 62 HOH HOH . E 5 HOH A 57 444 63 HOH HOH . E 5 HOH A 58 445 66 HOH HOH . E 5 HOH A 59 446 67 HOH HOH . E 5 HOH A 60 447 68 HOH HOH . E 5 HOH A 61 448 69 HOH HOH . E 5 HOH A 62 449 70 HOH HOH . E 5 HOH A 63 450 73 HOH HOH . E 5 HOH A 64 451 74 HOH HOH . E 5 HOH A 65 452 75 HOH HOH . E 5 HOH A 66 453 76 HOH HOH . E 5 HOH A 67 454 77 HOH HOH . E 5 HOH A 68 455 78 HOH HOH . E 5 HOH A 69 456 79 HOH HOH . E 5 HOH A 70 457 80 HOH HOH . E 5 HOH A 71 458 81 HOH HOH . E 5 HOH A 72 459 82 HOH HOH . E 5 HOH A 73 460 83 HOH HOH . E 5 HOH A 74 461 84 HOH HOH . E 5 HOH A 75 462 85 HOH HOH . E 5 HOH A 76 463 86 HOH HOH . E 5 HOH A 77 464 87 HOH HOH . E 5 HOH A 78 465 88 HOH HOH . E 5 HOH A 79 466 89 HOH HOH . E 5 HOH A 80 467 90 HOH HOH . E 5 HOH A 81 468 92 HOH HOH . E 5 HOH A 82 469 93 HOH HOH . E 5 HOH A 83 470 94 HOH HOH . E 5 HOH A 84 471 95 HOH HOH . E 5 HOH A 85 472 97 HOH HOH . E 5 HOH A 86 473 98 HOH HOH . E 5 HOH A 87 474 99 HOH HOH . E 5 HOH A 88 475 100 HOH HOH . E 5 HOH A 89 476 101 HOH HOH . E 5 HOH A 90 477 102 HOH HOH . E 5 HOH A 91 478 105 HOH HOH . E 5 HOH A 92 479 106 HOH HOH . E 5 HOH A 93 480 107 HOH HOH . E 5 HOH A 94 481 108 HOH HOH . E 5 HOH A 95 482 110 HOH HOH . E 5 HOH A 96 483 111 HOH HOH . E 5 HOH A 97 484 112 HOH HOH . E 5 HOH A 98 485 113 HOH HOH . E 5 HOH A 99 489 114 HOH HOH . E 5 HOH A 100 490 115 HOH HOH . E 5 HOH A 101 491 116 HOH HOH . E 5 HOH A 102 492 117 HOH HOH . E 5 HOH A 103 493 118 HOH HOH . E 5 HOH A 104 494 119 HOH HOH . E 5 HOH A 105 495 120 HOH HOH . E 5 HOH A 106 496 121 HOH HOH . E 5 HOH A 107 497 122 HOH HOH . E 5 HOH A 108 498 123 HOH HOH . E 5 HOH A 109 499 124 HOH HOH . E 5 HOH A 110 500 125 HOH HOH . E 5 HOH A 111 501 126 HOH HOH . E 5 HOH A 112 502 127 HOH HOH . E 5 HOH A 113 503 128 HOH HOH . E 5 HOH A 114 504 129 HOH HOH . E 5 HOH A 115 505 130 HOH HOH . E 5 HOH A 116 506 131 HOH HOH . E 5 HOH A 117 507 132 HOH HOH . E 5 HOH A 118 508 133 HOH HOH . E 5 HOH A 119 509 1 HOH HOH . E 5 HOH A 120 510 2 HOH HOH . E 5 HOH A 121 511 3 HOH HOH . E 5 HOH A 122 512 4 HOH HOH . E 5 HOH A 123 513 5 HOH HOH . E 5 HOH A 124 514 6 HOH HOH . E 5 HOH A 125 515 7 HOH HOH . E 5 HOH A 126 516 8 HOH HOH . E 5 HOH A 127 517 9 HOH HOH . E 5 HOH A 128 518 10 HOH HOH . E 5 HOH A 129 519 11 HOH HOH . E 5 HOH A 130 520 12 HOH HOH . E 5 HOH A 131 521 13 HOH HOH . E 5 HOH A 132 522 14 HOH HOH . E 5 HOH A 133 523 15 HOH HOH . E 5 HOH A 134 524 16 HOH HOH . E 5 HOH A 135 525 17 HOH HOH . E 5 HOH A 136 526 18 HOH HOH . E 5 HOH A 137 527 19 HOH HOH . E 5 HOH A 138 528 20 HOH HOH . E 5 HOH A 139 529 21 HOH HOH . E 5 HOH A 140 530 22 HOH HOH . E 5 HOH A 141 531 23 HOH HOH . E 5 HOH A 142 532 24 HOH HOH . E 5 HOH A 143 533 25 HOH HOH . E 5 HOH A 144 534 26 HOH HOH . E 5 HOH A 145 535 28 HOH HOH . E 5 HOH A 146 536 29 HOH HOH . E 5 HOH A 147 537 30 HOH HOH . E 5 HOH A 148 538 31 HOH HOH . E 5 HOH A 149 539 32 HOH HOH . E 5 HOH A 150 540 33 HOH HOH . E 5 HOH A 151 541 34 HOH HOH . E 5 HOH A 152 542 35 HOH HOH . E 5 HOH A 153 543 36 HOH HOH . E 5 HOH A 154 544 37 HOH HOH . E 5 HOH A 155 545 38 HOH HOH . E 5 HOH A 156 546 39 HOH HOH . E 5 HOH A 157 547 40 HOH HOH . E 5 HOH A 158 548 41 HOH HOH . E 5 HOH A 159 549 42 HOH HOH . E 5 HOH A 160 550 43 HOH HOH . E 5 HOH A 161 551 44 HOH HOH . E 5 HOH A 162 552 45 HOH HOH . E 5 HOH A 163 553 48 HOH HOH . E 5 HOH A 164 554 49 HOH HOH . E 5 HOH A 165 555 50 HOH HOH . E 5 HOH A 166 556 51 HOH HOH . E 5 HOH A 167 557 53 HOH HOH . E 5 HOH A 168 558 54 HOH HOH . E 5 HOH A 169 559 57 HOH HOH . E 5 HOH A 170 560 58 HOH HOH . E 5 HOH A 171 561 59 HOH HOH . E 5 HOH A 172 562 60 HOH HOH . E 5 HOH A 173 563 61 HOH HOH . E 5 HOH A 174 564 62 HOH HOH . E 5 HOH A 175 565 63 HOH HOH . E 5 HOH A 176 566 64 HOH HOH . E 5 HOH A 177 567 65 HOH HOH . E 5 HOH A 178 568 66 HOH HOH . E 5 HOH A 179 569 68 HOH HOH . E 5 HOH A 180 570 70 HOH HOH . E 5 HOH A 181 571 71 HOH HOH . E 5 HOH A 182 572 72 HOH HOH . E 5 HOH A 183 573 73 HOH HOH . E 5 HOH A 184 574 74 HOH HOH . E 5 HOH A 185 575 75 HOH HOH . E 5 HOH A 186 576 76 HOH HOH . E 5 HOH A 187 577 79 HOH HOH . E 5 HOH A 188 578 80 HOH HOH . E 5 HOH A 189 579 81 HOH HOH . E 5 HOH A 190 580 82 HOH HOH . E 5 HOH A 191 581 83 HOH HOH . E 5 HOH A 192 582 84 HOH HOH . E 5 HOH A 193 583 86 HOH HOH . E 5 HOH A 194 584 87 HOH HOH . E 5 HOH A 195 585 88 HOH HOH . E 5 HOH A 196 586 89 HOH HOH . E 5 HOH A 197 587 90 HOH HOH . E 5 HOH A 198 588 91 HOH HOH . E 5 HOH A 199 589 92 HOH HOH . E 5 HOH A 200 590 93 HOH HOH . E 5 HOH A 201 591 94 HOH HOH . E 5 HOH A 202 592 97 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 PB ADP . . . B 2 -4.55 -12.483 17.967 1 15.4 ? PB ADP 486 A 1 HETATM 2 O O1B ADP . . . B 2 -5.96 -12.738 17.483 1 14.5 ? O1B ADP 486 A 1 HETATM 3 O O2B ADP . . . B 2 -3.778 -11.392 17.254 1 11.72 ? O2B ADP 486 A 1 HETATM 4 O O3B ADP . . . B 2 -4.588 -12.43 19.479 1 14.35 ? O3B ADP 486 A 1 HETATM 5 P PA ADP . . . B 2 -3.266 -14.651 16.375 1 9.48 ? PA ADP 486 A 1 HETATM 6 O O1A ADP . . . B 2 -3.327 -13.755 15.174 1 9.52 ? O1A ADP 486 A 1 HETATM 7 O O2A ADP . . . B 2 -2.033 -15.399 16.824 1 8.73 ? O2A ADP 486 A 1 HETATM 8 O O3A ADP . . . B 2 -3.662 -13.812 17.717 1 11.7 ? O3A ADP 486 A 1 HETATM 9 O O5' ADP . . . B 2 -4.463 -15.726 16.27 1 7.47 ? O5' ADP 486 A 1 HETATM 10 C C5' ADP . . . B 2 -4.684 -16.674 17.303 1 6.85 ? C5' ADP 486 A 1 HETATM 11 C C4' ADP . . . B 2 -5.677 -17.671 16.741 1 9.92 ? C4' ADP 486 A 1 HETATM 12 O O4' ADP . . . B 2 -5.1 -18.331 15.599 1 8.7 ? O4' ADP 486 A 1 HETATM 13 C C3' ADP . . . B 2 -6.041 -18.733 17.767 1 8.51 ? C3' ADP 486 A 1 HETATM 14 O O3' ADP . . . B 2 -7.457 -18.822 17.798 1 7.68 ? O3' ADP 486 A 1 HETATM 15 C C2' ADP . . . B 2 -5.339 -19.963 17.225 1 9.71 ? C2' ADP 486 A 1 HETATM 16 O O2' ADP . . . B 2 -5.916 -21.221 17.591 1 11.32 ? O2' ADP 486 A 1 HETATM 17 C C1' ADP . . . B 2 -5.43 -19.689 15.737 1 10.87 ? C1' ADP 486 A 1 HETATM 18 N N9 ADP . . . B 2 -4.521 -20.465 14.878 1 13.39 ? N9 ADP 486 A 1 HETATM 19 C C8 ADP . . . B 2 -3.176 -20.477 14.916 1 12.88 ? C8 ADP 486 A 1 HETATM 20 N N7 ADP . . . B 2 -2.707 -21.303 13.96 1 14.24 ? N7 ADP 486 A 1 HETATM 21 C C5 ADP . . . B 2 -3.761 -21.794 13.298 1 14.02 ? C5 ADP 486 A 1 HETATM 22 C C6 ADP . . . B 2 -3.949 -22.73 12.184 1 15.39 ? C6 ADP 486 A 1 HETATM 23 N N6 ADP . . . B 2 -2.854 -23.266 11.587 1 19.08 ? N6 ADP 486 A 1 HETATM 24 N N1 ADP . . . B 2 -5.207 -22.988 11.793 1 14.64 ? N1 ADP 486 A 1 HETATM 25 C C2 ADP . . . B 2 -6.284 -22.443 12.404 1 15.45 ? C2 ADP 486 A 1 HETATM 26 N N3 ADP . . . B 2 -6.189 -21.58 13.437 1 15.22 ? N3 ADP 486 A 1 HETATM 27 C C4 ADP . . . B 2 -4.963 -21.235 13.908 1 13.82 ? C4 ADP 486 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #