data_5T3O # _model_server_result.job_id Rm-pJXMNx2UWWztRbWH8-w _model_server_result.datetime_utc '2024-12-21 12:39:05' _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 5t3o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 5T3O # _exptl.entry_id 5T3O _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 3 _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 5T3O _cell.length_a 115.97 _cell.length_b 115.97 _cell.length_c 207.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T3O _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,F,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 G N N ? 2 J N N # _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 5T3O _atom_sites.fract_transf_matrix[1][1] 0.008623 _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] 0.008623 _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] 0.004808 _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 D 2 ADP A 1 401 3 ADP ADP . E 3 SO4 A 1 402 3 SO4 SO4 . F 3 SO4 A 1 403 6 SO4 SO4 . G 2 ADP B 1 401 1 ADP ADP . H 3 SO4 B 1 402 2 SO4 SO4 . I 3 SO4 B 1 403 4 SO4 SO4 . J 2 ADP C 1 401 2 ADP ADP . K 3 SO4 C 1 402 1 SO4 SO4 . L 3 SO4 C 1 403 5 SO4 SO4 . M 4 HOH A 1 501 173 HOH HOH . M 4 HOH A 2 502 43 HOH HOH . M 4 HOH A 3 503 172 HOH HOH . M 4 HOH A 4 504 2 HOH HOH . M 4 HOH A 5 505 103 HOH HOH . M 4 HOH A 6 506 41 HOH HOH . M 4 HOH A 7 507 64 HOH HOH . M 4 HOH A 8 508 143 HOH HOH . M 4 HOH A 9 509 40 HOH HOH . M 4 HOH A 10 510 1 HOH HOH . M 4 HOH A 11 511 174 HOH HOH . M 4 HOH A 12 512 178 HOH HOH . M 4 HOH A 13 513 176 HOH HOH . M 4 HOH A 14 514 59 HOH HOH . M 4 HOH A 15 515 27 HOH HOH . M 4 HOH A 16 516 123 HOH HOH . M 4 HOH A 17 517 131 HOH HOH . M 4 HOH A 18 518 145 HOH HOH . M 4 HOH A 19 519 69 HOH HOH . M 4 HOH A 20 520 121 HOH HOH . M 4 HOH A 21 521 96 HOH HOH . M 4 HOH A 22 522 198 HOH HOH . M 4 HOH A 23 523 138 HOH HOH . M 4 HOH A 24 524 70 HOH HOH . M 4 HOH A 25 525 106 HOH HOH . M 4 HOH A 26 526 125 HOH HOH . M 4 HOH A 27 527 55 HOH HOH . M 4 HOH A 28 528 111 HOH HOH . M 4 HOH A 29 529 171 HOH HOH . N 4 HOH B 1 501 75 HOH HOH . N 4 HOH B 2 502 116 HOH HOH . N 4 HOH B 3 503 113 HOH HOH . N 4 HOH B 4 504 100 HOH HOH . N 4 HOH B 5 505 65 HOH HOH . N 4 HOH B 6 506 15 HOH HOH . N 4 HOH B 7 507 183 HOH HOH . N 4 HOH B 8 508 9 HOH HOH . N 4 HOH B 9 509 56 HOH HOH . N 4 HOH B 10 510 47 HOH HOH . N 4 HOH B 11 511 32 HOH HOH . N 4 HOH B 12 512 5 HOH HOH . N 4 HOH B 13 513 21 HOH HOH . N 4 HOH B 14 514 22 HOH HOH . N 4 HOH B 15 515 166 HOH HOH . N 4 HOH B 16 516 68 HOH HOH . N 4 HOH B 17 517 13 HOH HOH . N 4 HOH B 18 518 50 HOH HOH . N 4 HOH B 19 519 130 HOH HOH . N 4 HOH B 20 520 146 HOH HOH . N 4 HOH B 21 521 196 HOH HOH . N 4 HOH B 22 522 66 HOH HOH . N 4 HOH B 23 523 163 HOH HOH . N 4 HOH B 24 524 7 HOH HOH . N 4 HOH B 25 525 158 HOH HOH . N 4 HOH B 26 526 165 HOH HOH . N 4 HOH B 27 527 89 HOH HOH . N 4 HOH B 28 528 14 HOH HOH . N 4 HOH B 29 529 120 HOH HOH . N 4 HOH B 30 530 30 HOH HOH . N 4 HOH B 31 531 23 HOH HOH . N 4 HOH B 32 532 72 HOH HOH . N 4 HOH B 33 533 179 HOH HOH . N 4 HOH B 34 534 94 HOH HOH . N 4 HOH B 35 535 57 HOH HOH . N 4 HOH B 36 536 197 HOH HOH . N 4 HOH B 37 537 184 HOH HOH . N 4 HOH B 38 538 49 HOH HOH . N 4 HOH B 39 539 144 HOH HOH . N 4 HOH B 40 540 81 HOH HOH . N 4 HOH B 41 541 118 HOH HOH . N 4 HOH B 42 542 26 HOH HOH . N 4 HOH B 43 543 42 HOH HOH . N 4 HOH B 44 544 175 HOH HOH . N 4 HOH B 45 545 153 HOH HOH . N 4 HOH B 46 546 20 HOH HOH . N 4 HOH B 47 547 126 HOH HOH . N 4 HOH B 48 548 60 HOH HOH . N 4 HOH B 49 549 129 HOH HOH . N 4 HOH B 50 550 45 HOH HOH . N 4 HOH B 51 551 148 HOH HOH . N 4 HOH B 52 552 195 HOH HOH . N 4 HOH B 53 553 29 HOH HOH . N 4 HOH B 54 554 97 HOH HOH . N 4 HOH B 55 555 149 HOH HOH . N 4 HOH B 56 556 37 HOH HOH . N 4 HOH B 57 557 160 HOH HOH . N 4 HOH B 58 558 51 HOH HOH . N 4 HOH B 59 559 162 HOH HOH . N 4 HOH B 60 560 159 HOH HOH . N 4 HOH B 61 561 151 HOH HOH . N 4 HOH B 62 562 167 HOH HOH . N 4 HOH B 63 563 46 HOH HOH . N 4 HOH B 64 564 99 HOH HOH . N 4 HOH B 65 565 182 HOH HOH . N 4 HOH B 66 566 10 HOH HOH . N 4 HOH B 67 567 19 HOH HOH . N 4 HOH B 68 568 33 HOH HOH . N 4 HOH B 69 569 132 HOH HOH . N 4 HOH B 70 570 128 HOH HOH . N 4 HOH B 71 571 18 HOH HOH . N 4 HOH B 72 572 133 HOH HOH . N 4 HOH B 73 573 193 HOH HOH . N 4 HOH B 74 574 154 HOH HOH . N 4 HOH B 75 575 152 HOH HOH . N 4 HOH B 76 576 86 HOH HOH . N 4 HOH B 77 577 63 HOH HOH . N 4 HOH B 78 578 52 HOH HOH . N 4 HOH B 79 579 137 HOH HOH . N 4 HOH B 80 580 76 HOH HOH . N 4 HOH B 81 581 25 HOH HOH . N 4 HOH B 82 582 84 HOH HOH . N 4 HOH B 83 583 105 HOH HOH . N 4 HOH B 84 584 194 HOH HOH . N 4 HOH B 85 585 157 HOH HOH . N 4 HOH B 86 586 185 HOH HOH . N 4 HOH B 87 587 16 HOH HOH . N 4 HOH B 88 588 92 HOH HOH . N 4 HOH B 89 589 90 HOH HOH . N 4 HOH B 90 590 142 HOH HOH . N 4 HOH B 91 591 91 HOH HOH . N 4 HOH B 92 592 164 HOH HOH . N 4 HOH B 93 593 139 HOH HOH . N 4 HOH B 94 594 77 HOH HOH . N 4 HOH B 95 595 79 HOH HOH . N 4 HOH B 96 596 3 HOH HOH . N 4 HOH B 97 597 38 HOH HOH . N 4 HOH B 98 598 117 HOH HOH . N 4 HOH B 99 599 74 HOH HOH . N 4 HOH B 100 600 17 HOH HOH . N 4 HOH B 101 601 181 HOH HOH . N 4 HOH B 102 602 87 HOH HOH . O 4 HOH C 1 501 48 HOH HOH . O 4 HOH C 2 502 39 HOH HOH . O 4 HOH C 3 503 192 HOH HOH . O 4 HOH C 4 504 53 HOH HOH . O 4 HOH C 5 505 114 HOH HOH . O 4 HOH C 6 506 80 HOH HOH . O 4 HOH C 7 507 71 HOH HOH . O 4 HOH C 8 508 189 HOH HOH . O 4 HOH C 9 509 95 HOH HOH . O 4 HOH C 10 510 134 HOH HOH . O 4 HOH C 11 511 34 HOH HOH . O 4 HOH C 12 512 190 HOH HOH . O 4 HOH C 13 513 161 HOH HOH . O 4 HOH C 14 514 156 HOH HOH . O 4 HOH C 15 515 24 HOH HOH . O 4 HOH C 16 516 187 HOH HOH . O 4 HOH C 17 517 58 HOH HOH . O 4 HOH C 18 518 31 HOH HOH . O 4 HOH C 19 519 104 HOH HOH . O 4 HOH C 20 520 98 HOH HOH . O 4 HOH C 21 521 112 HOH HOH . O 4 HOH C 22 522 12 HOH HOH . O 4 HOH C 23 523 168 HOH HOH . O 4 HOH C 24 524 169 HOH HOH . O 4 HOH C 25 525 6 HOH HOH . O 4 HOH C 26 526 188 HOH HOH . O 4 HOH C 27 527 102 HOH HOH . O 4 HOH C 28 528 186 HOH HOH . O 4 HOH C 29 529 62 HOH HOH . O 4 HOH C 30 530 109 HOH HOH . O 4 HOH C 31 531 155 HOH HOH . O 4 HOH C 32 532 135 HOH HOH . O 4 HOH C 33 533 191 HOH HOH . O 4 HOH C 34 534 124 HOH HOH . O 4 HOH C 35 535 141 HOH HOH . O 4 HOH C 36 536 4 HOH HOH . O 4 HOH C 37 537 61 HOH HOH . O 4 HOH C 38 538 93 HOH HOH . O 4 HOH C 39 539 28 HOH HOH . O 4 HOH C 40 540 82 HOH HOH . O 4 HOH C 41 541 147 HOH HOH . O 4 HOH C 42 542 83 HOH HOH . O 4 HOH C 43 543 44 HOH HOH . O 4 HOH C 44 544 85 HOH HOH . O 4 HOH C 45 545 35 HOH HOH . O 4 HOH C 46 546 107 HOH HOH . O 4 HOH C 47 547 88 HOH HOH . O 4 HOH C 48 548 122 HOH HOH . O 4 HOH C 49 549 67 HOH HOH . O 4 HOH C 50 550 101 HOH HOH . O 4 HOH C 51 551 140 HOH HOH . O 4 HOH C 52 552 119 HOH HOH . O 4 HOH C 53 553 73 HOH HOH . O 4 HOH C 54 554 36 HOH HOH . O 4 HOH C 55 555 136 HOH HOH . O 4 HOH C 56 556 78 HOH HOH . O 4 HOH C 57 557 115 HOH HOH . O 4 HOH C 58 558 150 HOH HOH . O 4 HOH C 59 559 110 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 . . . J 2 -0.721 -44.738 0.492 1 79.47 ? PB ADP 401 C 1 HETATM 2 O O1B ADP . . . J 2 -0.416 -45.545 -0.751 1 81.72 ? O1B ADP 401 C 1 HETATM 3 O O2B ADP . . . J 2 -1.961 -45.196 1.233 1 79.77 ? O2B ADP 401 C 1 HETATM 4 O O3B ADP . . . J 2 -0.645 -43.247 0.278 1 81.24 ? O3B ADP 401 C 1 HETATM 5 P PA ADP . . . J 2 0.748 -44.442 2.947 1 74.36 ? PA ADP 401 C 1 HETATM 6 O O1A ADP . . . J 2 1.936 -45.15 3.557 1 76.84 ? O1A ADP 401 C 1 HETATM 7 O O2A ADP . . . J 2 -0.572 -44.445 3.68 1 74.44 ? O2A ADP 401 C 1 HETATM 8 O O3A ADP . . . J 2 0.54 -45.043 1.459 1 77.52 ? O3A ADP 401 C 1 HETATM 9 O O5' ADP . . . J 2 1.193 -42.919 2.702 1 67.75 ? O5' ADP 401 C 1 HETATM 10 C C5' ADP . . . J 2 1.353 -42.019 3.796 1 63.41 ? C5' ADP 401 C 1 HETATM 11 C C4' ADP . . . J 2 2.82 -41.962 4.214 1 58.71 ? C4' ADP 401 C 1 HETATM 12 O O4' ADP . . . J 2 3.533 -41.111 3.317 1 53.59 ? O4' ADP 401 C 1 HETATM 13 C C3' ADP . . . J 2 3.005 -41.399 5.619 1 57.33 ? C3' ADP 401 C 1 HETATM 14 O O3' ADP . . . J 2 3.936 -42.207 6.351 1 61.58 ? O3' ADP 401 C 1 HETATM 15 C C2' ADP . . . J 2 3.523 -39.989 5.431 1 53.3 ? C2' ADP 401 C 1 HETATM 16 O O2' ADP . . . J 2 4.566 -39.678 6.362 1 55.79 ? O2' ADP 401 C 1 HETATM 17 C C1' ADP . . . J 2 4.047 -39.96 3.992 1 50.78 ? C1' ADP 401 C 1 HETATM 18 N N9 ADP . . . J 2 3.674 -38.757 3.203 1 45.2 ? N9 ADP 401 C 1 HETATM 19 C C8 ADP . . . J 2 2.57 -37.984 3.333 1 42.74 ? C8 ADP 401 C 1 HETATM 20 N N7 ADP . . . J 2 2.575 -36.981 2.427 1 40.09 ? N7 ADP 401 C 1 HETATM 21 C C5 ADP . . . J 2 3.68 -37.111 1.686 1 38.73 ? C5 ADP 401 C 1 HETATM 22 C C6 ADP . . . J 2 4.288 -36.375 0.558 1 37.07 ? C6 ADP 401 C 1 HETATM 23 N N6 ADP . . . J 2 3.666 -35.294 0.056 1 36.09 ? N6 ADP 401 C 1 HETATM 24 N N1 ADP . . . J 2 5.468 -36.817 0.064 1 36.6 ? N1 ADP 401 C 1 HETATM 25 C C2 ADP . . . J 2 6.082 -37.905 0.575 1 36.81 ? C2 ADP 401 C 1 HETATM 26 N N3 ADP . . . J 2 5.578 -38.616 1.601 1 38.29 ? N3 ADP 401 C 1 HETATM 27 C C4 ADP . . . J 2 4.406 -38.279 2.195 1 40.51 ? C4 ADP 401 C 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #