data_6BQ3 # _model_server_result.job_id Dj0X_ivS1qZjnyrWtVJwZg _model_server_result.datetime_utc '2024-11-25 02:59:22' _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 6bq3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 6BQ3 # _exptl.entry_id 6BQ3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.401 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-(3-aminopropyl)-5'-thioadenosine" _entity.pdbx_number_of_molecules 2 _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 6BQ3 _cell.length_a 81.052 _cell.length_b 81.052 _cell.length_c 163.128 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BQ3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 C N N ? 2 D N N # _chem_comp.formula 'C13 H20 N6 O3 S' _chem_comp.formula_weight 340.401 _chem_comp.id DSH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-(3-aminopropyl)-5'-thioadenosine" _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 N CA DSH sing 83 n n N1 C2 DSH doub 84 n y N1 C6 DSH sing 85 n y C2 N3 DSH sing 86 n y N3 C4 DSH doub 87 n y C4 C5 DSH sing 88 n y C4 N9 DSH sing 89 n y C5 C6 DSH doub 90 n y C5 N7 DSH sing 91 n y C6 N6 DSH sing 92 n n N7 C8 DSH doub 93 n y C8 N9 DSH sing 94 n y N9 C1' DSH sing 95 n n CA CB DSH sing 96 n n CB CG DSH sing 97 n n SD CG DSH sing 98 n n SD C5' DSH sing 99 n n C1' C2' DSH sing 100 n n C1' O4' DSH sing 101 n n C2' O2' DSH sing 102 n n C2' C3' DSH sing 103 n n C3' O3' DSH sing 104 n n C3' C4' DSH sing 105 n n C4' O4' DSH sing 106 n n C4' C5' DSH sing 107 n n N HN DSH sing 108 n n N HNA DSH sing 109 n n C2 H2 DSH sing 110 n n N6 HN6 DSH sing 111 n n N6 HN6A DSH sing 112 n n C8 H8 DSH sing 113 n n CA HA DSH sing 114 n n CB HB DSH sing 115 n n CG HG DSH sing 116 n n CG HGA DSH sing 117 n n C1' H1' DSH sing 118 n n C2' H2' DSH sing 119 n n O2' HO2' DSH sing 120 n n C3' H3' DSH sing 121 n n O3' HO3' DSH sing 122 n n C4' H4' DSH sing 123 n n C5' H5' DSH sing 124 n n C5' "H5'A" DSH sing 125 n n CA HAA DSH sing 126 n n CB HBA DSH sing 127 n n # _atom_sites.entry_id 6BQ3 _atom_sites.fract_transf_matrix[1][1] 0.012338 _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] 0.012338 _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] 0.00613 _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 C 2 DSH A 1 401 2 DSH DSH . D 2 DSH B 1 401 1 DSH DSH . E 3 HOH A 1 501 22 HOH HOH . E 3 HOH A 2 502 112 HOH HOH . E 3 HOH A 3 503 141 HOH HOH . E 3 HOH A 4 504 117 HOH HOH . E 3 HOH A 5 505 84 HOH HOH . E 3 HOH A 6 506 170 HOH HOH . E 3 HOH A 7 507 81 HOH HOH . E 3 HOH A 8 508 12 HOH HOH . E 3 HOH A 9 509 111 HOH HOH . E 3 HOH A 10 510 147 HOH HOH . E 3 HOH A 11 511 15 HOH HOH . E 3 HOH A 12 512 178 HOH HOH . E 3 HOH A 13 513 158 HOH HOH . E 3 HOH A 14 514 23 HOH HOH . E 3 HOH A 15 515 93 HOH HOH . E 3 HOH A 16 516 151 HOH HOH . E 3 HOH A 17 517 82 HOH HOH . E 3 HOH A 18 518 13 HOH HOH . E 3 HOH A 19 519 87 HOH HOH . E 3 HOH A 20 520 179 HOH HOH . E 3 HOH A 21 521 7 HOH HOH . E 3 HOH A 22 522 172 HOH HOH . E 3 HOH A 23 523 184 HOH HOH . E 3 HOH A 24 524 21 HOH HOH . E 3 HOH A 25 525 17 HOH HOH . E 3 HOH A 26 526 67 HOH HOH . E 3 HOH A 27 527 5 HOH HOH . E 3 HOH A 28 528 105 HOH HOH . E 3 HOH A 29 529 171 HOH HOH . E 3 HOH A 30 530 121 HOH HOH . E 3 HOH A 31 531 2 HOH HOH . E 3 HOH A 32 532 89 HOH HOH . E 3 HOH A 33 533 32 HOH HOH . E 3 HOH A 34 534 10 HOH HOH . E 3 HOH A 35 535 14 HOH HOH . E 3 HOH A 36 536 20 HOH HOH . E 3 HOH A 37 537 8 HOH HOH . E 3 HOH A 38 538 86 HOH HOH . E 3 HOH A 39 539 180 HOH HOH . E 3 HOH A 40 540 29 HOH HOH . E 3 HOH A 41 541 47 HOH HOH . E 3 HOH A 42 542 52 HOH HOH . E 3 HOH A 43 543 102 HOH HOH . E 3 HOH A 44 544 53 HOH HOH . E 3 HOH A 45 545 9 HOH HOH . E 3 HOH A 46 546 104 HOH HOH . E 3 HOH A 47 547 90 HOH HOH . E 3 HOH A 48 548 173 HOH HOH . E 3 HOH A 49 549 142 HOH HOH . E 3 HOH A 50 550 4 HOH HOH . E 3 HOH A 51 551 110 HOH HOH . E 3 HOH A 52 552 65 HOH HOH . E 3 HOH A 53 553 183 HOH HOH . E 3 HOH A 54 554 98 HOH HOH . E 3 HOH A 55 555 46 HOH HOH . E 3 HOH A 56 556 77 HOH HOH . E 3 HOH A 57 557 122 HOH HOH . E 3 HOH A 58 558 101 HOH HOH . E 3 HOH A 59 559 150 HOH HOH . E 3 HOH A 60 560 182 HOH HOH . F 3 HOH B 1 501 70 HOH HOH . F 3 HOH B 2 502 114 HOH HOH . F 3 HOH B 3 503 131 HOH HOH . F 3 HOH B 4 504 68 HOH HOH . F 3 HOH B 5 505 71 HOH HOH . F 3 HOH B 6 506 120 HOH HOH . F 3 HOH B 7 507 139 HOH HOH . F 3 HOH B 8 508 106 HOH HOH . F 3 HOH B 9 509 48 HOH HOH . F 3 HOH B 10 510 92 HOH HOH . F 3 HOH B 11 511 165 HOH HOH . F 3 HOH B 12 512 91 HOH HOH . F 3 HOH B 13 513 144 HOH HOH . F 3 HOH B 14 514 118 HOH HOH . F 3 HOH B 15 515 113 HOH HOH . F 3 HOH B 16 516 72 HOH HOH . F 3 HOH B 17 517 181 HOH HOH . F 3 HOH B 18 518 137 HOH HOH . F 3 HOH B 19 519 177 HOH HOH . F 3 HOH B 20 520 176 HOH HOH . F 3 HOH B 21 521 40 HOH HOH . F 3 HOH B 22 522 1 HOH HOH . F 3 HOH B 23 523 166 HOH HOH . F 3 HOH B 24 524 3 HOH HOH . F 3 HOH B 25 525 127 HOH HOH . F 3 HOH B 26 526 24 HOH HOH . F 3 HOH B 27 527 168 HOH HOH . F 3 HOH B 28 528 80 HOH HOH . F 3 HOH B 29 529 159 HOH HOH . F 3 HOH B 30 530 11 HOH HOH . F 3 HOH B 31 531 50 HOH HOH . F 3 HOH B 32 532 60 HOH HOH . F 3 HOH B 33 533 25 HOH HOH . F 3 HOH B 34 534 136 HOH HOH . F 3 HOH B 35 535 115 HOH HOH . F 3 HOH B 36 536 41 HOH HOH . F 3 HOH B 37 537 88 HOH HOH . F 3 HOH B 38 538 44 HOH HOH . F 3 HOH B 39 539 33 HOH HOH . F 3 HOH B 40 540 149 HOH HOH . F 3 HOH B 41 541 154 HOH HOH . F 3 HOH B 42 542 185 HOH HOH . F 3 HOH B 43 543 66 HOH HOH . F 3 HOH B 44 544 45 HOH HOH . F 3 HOH B 45 545 64 HOH HOH . F 3 HOH B 46 546 43 HOH HOH . F 3 HOH B 47 547 148 HOH HOH . F 3 HOH B 48 548 187 HOH HOH . F 3 HOH B 49 549 74 HOH HOH . F 3 HOH B 50 550 78 HOH HOH . F 3 HOH B 51 551 116 HOH HOH . F 3 HOH B 52 552 42 HOH HOH . F 3 HOH B 53 553 94 HOH HOH . F 3 HOH B 54 554 107 HOH HOH . F 3 HOH B 55 555 63 HOH HOH . F 3 HOH B 56 556 58 HOH HOH . F 3 HOH B 57 557 26 HOH HOH . F 3 HOH B 58 558 62 HOH HOH . F 3 HOH B 59 559 157 HOH HOH . F 3 HOH B 60 560 36 HOH HOH . F 3 HOH B 61 561 75 HOH HOH . F 3 HOH B 62 562 16 HOH HOH . F 3 HOH B 63 563 57 HOH HOH . F 3 HOH B 64 564 143 HOH HOH . F 3 HOH B 65 565 134 HOH HOH . F 3 HOH B 66 566 125 HOH HOH . F 3 HOH B 67 567 69 HOH HOH . F 3 HOH B 68 568 79 HOH HOH . F 3 HOH B 69 569 56 HOH HOH . F 3 HOH B 70 570 31 HOH HOH . F 3 HOH B 71 571 27 HOH HOH . F 3 HOH B 72 572 83 HOH HOH . F 3 HOH B 73 573 59 HOH HOH . F 3 HOH B 74 574 30 HOH HOH . F 3 HOH B 75 575 6 HOH HOH . F 3 HOH B 76 576 138 HOH HOH . F 3 HOH B 77 577 109 HOH HOH . F 3 HOH B 78 578 35 HOH HOH . F 3 HOH B 79 579 97 HOH HOH . F 3 HOH B 80 580 28 HOH HOH . F 3 HOH B 81 581 132 HOH HOH . F 3 HOH B 82 582 54 HOH HOH . F 3 HOH B 83 583 37 HOH HOH . F 3 HOH B 84 584 169 HOH HOH . F 3 HOH B 85 585 119 HOH HOH . F 3 HOH B 86 586 103 HOH HOH . F 3 HOH B 87 587 19 HOH HOH . F 3 HOH B 88 588 135 HOH HOH . F 3 HOH B 89 589 164 HOH HOH . F 3 HOH B 90 590 49 HOH HOH . F 3 HOH B 91 591 155 HOH HOH . F 3 HOH B 92 592 123 HOH HOH . F 3 HOH B 93 593 51 HOH HOH . F 3 HOH B 94 594 85 HOH HOH . F 3 HOH B 95 595 100 HOH HOH . F 3 HOH B 96 596 95 HOH HOH . F 3 HOH B 97 597 124 HOH HOH . F 3 HOH B 98 598 174 HOH HOH . F 3 HOH B 99 599 96 HOH HOH . F 3 HOH B 100 600 175 HOH HOH . F 3 HOH B 101 601 108 HOH HOH . F 3 HOH B 102 602 99 HOH HOH . F 3 HOH B 103 603 186 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 N N DSH . . . D 2 20.557 39.232 17.722 1 49.9 ? N DSH 401 B 1 HETATM 2 N N1 DSH . . . D 2 24.284 51.628 16.757 1 30.2 ? N1 DSH 401 B 1 HETATM 3 C C2 DSH . . . D 2 22.887 51.399 16.814 1 29.05 ? C2 DSH 401 B 1 HETATM 4 N N3 DSH . . . D 2 22.332 50.222 16.166 1 29.85 ? N3 DSH 401 B 1 HETATM 5 C C4 DSH . . . D 2 23.231 49.297 15.417 1 29.95 ? C4 DSH 401 B 1 HETATM 6 C C5 DSH . . . D 2 24.571 49.515 15.359 1 30.45 ? C5 DSH 401 B 1 HETATM 7 C C6 DSH . . . D 2 25.155 50.738 16.063 1 31.61 ? C6 DSH 401 B 1 HETATM 8 N N6 DSH . . . D 2 26.562 51.011 16.038 1 30.48 ? N6 DSH 401 B 1 HETATM 9 N N7 DSH . . . D 2 25.124 48.528 14.645 1 30.64 ? N7 DSH 401 B 1 HETATM 10 C C8 DSH . . . D 2 24.13 47.692 14.244 1 29.59 ? C8 DSH 401 B 1 HETATM 11 N N9 DSH . . . D 2 22.944 48.173 14.735 1 31.6 ? N9 DSH 401 B 1 HETATM 12 C CA DSH . . . D 2 20.424 40.679 17.92 1 46.9 ? CA DSH 401 B 1 HETATM 13 C CB DSH . . . D 2 20.925 41.474 16.699 1 44.7 ? CB DSH 401 B 1 HETATM 14 S SD DSH . . . D 2 20.534 42.863 14.426 1 39.47 ? SD DSH 401 B 1 HETATM 15 C CG DSH . . . D 2 19.785 42.174 15.936 1 41.65 ? CG DSH 401 B 1 HETATM 16 C C1' DSH . . . D 2 21.706 47.668 14.628 1 31.63 ? C1' DSH 401 B 1 HETATM 17 C C2' DSH . . . D 2 21.268 47.037 13.236 1 32.97 ? C2' DSH 401 B 1 HETATM 18 O O2' DSH . . . D 2 20.737 48.144 12.389 1 29.47 ? O2' DSH 401 B 1 HETATM 19 C C3' DSH . . . D 2 20.382 46.177 13.534 1 31.39 ? C3' DSH 401 B 1 HETATM 20 O O3' DSH . . . D 2 19.039 46.725 13.737 1 32.69 ? O3' DSH 401 B 1 HETATM 21 C C4' DSH . . . D 2 20.837 45.576 14.997 1 33.99 ? C4' DSH 401 B 1 HETATM 22 O O4' DSH . . . D 2 21.575 46.506 15.57 1 31.74 ? O4' DSH 401 B 1 HETATM 23 C C5' DSH . . . D 2 21.626 44.298 14.789 1 34.11 ? C5' DSH 401 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #