data_5IS7 # _model_server_result.job_id zDNvoKBlKh1dRhZPZmvZEw _model_server_result.datetime_utc '2024-11-16 10:25:11' _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 5is7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":503}' # _entry.id 5IS7 # _exptl.entry_id 5IS7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.401 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-(3-aminopropyl)-5'-thioadenosine" _entity.pdbx_number_of_molecules 4 _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 5IS7 _cell.length_a 74.528 _cell.length_b 98.935 _cell.length_c 206.914 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IS7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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,P,Q,R,S _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 K N N ? 4 M N N ? 4 O 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 5IS7 _atom_sites.fract_transf_matrix[1][1] 0.013418 _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] 0.010108 _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] 0.004833 _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 E 2 EDO A 1 501 4 EDO EDO . F 3 PEG A 1 502 6 PEG PEG . G 3 PEG A 1 503 7 PEG PEG . H 4 DSH A 1 504 1 DSH DSH . I 2 EDO B 1 501 2 EDO EDO . J 2 EDO B 1 502 3 EDO EDO . K 4 DSH B 1 503 2 DSH DSH . L 2 EDO C 1 501 1 EDO EDO . M 4 DSH C 1 502 3 DSH DSH . N 2 EDO D 1 501 5 EDO EDO . O 4 DSH D 1 502 4 DSH DSH . P 5 HOH A 1 601 30 HOH HOH . P 5 HOH A 2 602 12 HOH HOH . P 5 HOH A 3 603 104 HOH HOH . P 5 HOH A 4 604 94 HOH HOH . P 5 HOH A 5 605 37 HOH HOH . P 5 HOH A 6 606 79 HOH HOH . P 5 HOH A 7 607 35 HOH HOH . P 5 HOH A 8 608 65 HOH HOH . P 5 HOH A 9 609 31 HOH HOH . P 5 HOH A 10 610 119 HOH HOH . P 5 HOH A 11 611 28 HOH HOH . P 5 HOH A 12 612 74 HOH HOH . P 5 HOH A 13 613 106 HOH HOH . P 5 HOH A 14 614 8 HOH HOH . P 5 HOH A 15 615 6 HOH HOH . P 5 HOH A 16 616 105 HOH HOH . P 5 HOH A 17 617 26 HOH HOH . P 5 HOH A 18 618 111 HOH HOH . P 5 HOH A 19 619 96 HOH HOH . P 5 HOH A 20 620 5 HOH HOH . P 5 HOH A 21 621 39 HOH HOH . P 5 HOH A 22 622 13 HOH HOH . P 5 HOH A 23 623 101 HOH HOH . P 5 HOH A 24 624 80 HOH HOH . P 5 HOH A 25 625 23 HOH HOH . P 5 HOH A 26 626 46 HOH HOH . P 5 HOH A 27 627 48 HOH HOH . P 5 HOH A 28 628 10 HOH HOH . P 5 HOH A 29 629 83 HOH HOH . P 5 HOH A 30 630 18 HOH HOH . P 5 HOH A 31 631 9 HOH HOH . P 5 HOH A 32 632 42 HOH HOH . P 5 HOH A 33 633 52 HOH HOH . P 5 HOH A 34 634 4 HOH HOH . P 5 HOH A 35 635 103 HOH HOH . P 5 HOH A 36 636 45 HOH HOH . P 5 HOH A 37 637 38 HOH HOH . P 5 HOH A 38 638 21 HOH HOH . P 5 HOH A 39 639 60 HOH HOH . P 5 HOH A 40 640 86 HOH HOH . P 5 HOH A 41 641 36 HOH HOH . P 5 HOH A 42 642 25 HOH HOH . P 5 HOH A 43 643 116 HOH HOH . P 5 HOH A 44 644 57 HOH HOH . P 5 HOH A 45 645 81 HOH HOH . P 5 HOH A 46 646 99 HOH HOH . P 5 HOH A 47 647 67 HOH HOH . P 5 HOH A 48 648 118 HOH HOH . P 5 HOH A 49 649 63 HOH HOH . P 5 HOH A 50 650 114 HOH HOH . P 5 HOH A 51 651 120 HOH HOH . P 5 HOH A 52 652 91 HOH HOH . P 5 HOH A 53 653 115 HOH HOH . P 5 HOH A 54 654 59 HOH HOH . P 5 HOH A 55 655 40 HOH HOH . P 5 HOH A 56 656 82 HOH HOH . P 5 HOH A 57 657 117 HOH HOH . P 5 HOH A 58 658 84 HOH HOH . P 5 HOH A 59 659 100 HOH HOH . P 5 HOH A 60 660 53 HOH HOH . P 5 HOH A 61 661 110 HOH HOH . Q 5 HOH B 1 601 2 HOH HOH . Q 5 HOH B 2 602 3 HOH HOH . Q 5 HOH B 3 603 108 HOH HOH . Q 5 HOH B 4 604 107 HOH HOH . Q 5 HOH B 5 605 44 HOH HOH . Q 5 HOH B 6 606 77 HOH HOH . Q 5 HOH B 7 607 24 HOH HOH . Q 5 HOH B 8 608 49 HOH HOH . Q 5 HOH B 9 609 43 HOH HOH . Q 5 HOH B 10 610 71 HOH HOH . Q 5 HOH B 11 611 1 HOH HOH . Q 5 HOH B 12 612 33 HOH HOH . Q 5 HOH B 13 613 14 HOH HOH . Q 5 HOH B 14 614 15 HOH HOH . Q 5 HOH B 15 615 7 HOH HOH . Q 5 HOH B 16 616 95 HOH HOH . Q 5 HOH B 17 617 51 HOH HOH . Q 5 HOH B 18 618 58 HOH HOH . Q 5 HOH B 19 619 27 HOH HOH . Q 5 HOH B 20 620 47 HOH HOH . Q 5 HOH B 21 621 70 HOH HOH . Q 5 HOH B 22 622 56 HOH HOH . Q 5 HOH B 23 623 32 HOH HOH . Q 5 HOH B 24 624 98 HOH HOH . Q 5 HOH B 25 625 19 HOH HOH . Q 5 HOH B 26 626 92 HOH HOH . Q 5 HOH B 27 627 90 HOH HOH . Q 5 HOH B 28 628 34 HOH HOH . Q 5 HOH B 29 629 62 HOH HOH . Q 5 HOH B 30 630 54 HOH HOH . Q 5 HOH B 31 631 22 HOH HOH . Q 5 HOH B 32 632 88 HOH HOH . Q 5 HOH B 33 633 66 HOH HOH . Q 5 HOH B 34 634 85 HOH HOH . Q 5 HOH B 35 635 29 HOH HOH . Q 5 HOH B 36 636 73 HOH HOH . Q 5 HOH B 37 637 61 HOH HOH . Q 5 HOH B 38 638 55 HOH HOH . Q 5 HOH B 39 639 41 HOH HOH . Q 5 HOH B 40 640 113 HOH HOH . Q 5 HOH B 41 641 102 HOH HOH . Q 5 HOH B 42 642 75 HOH HOH . Q 5 HOH B 43 643 69 HOH HOH . Q 5 HOH B 44 644 76 HOH HOH . R 5 HOH C 1 601 50 HOH HOH . R 5 HOH C 2 602 11 HOH HOH . R 5 HOH C 3 603 64 HOH HOH . R 5 HOH C 4 604 17 HOH HOH . R 5 HOH C 5 605 16 HOH HOH . R 5 HOH C 6 606 72 HOH HOH . R 5 HOH C 7 607 78 HOH HOH . R 5 HOH C 8 608 97 HOH HOH . R 5 HOH C 9 609 68 HOH HOH . R 5 HOH C 10 610 93 HOH HOH . R 5 HOH C 11 611 87 HOH HOH . S 5 HOH D 1 601 109 HOH HOH . S 5 HOH D 2 602 89 HOH HOH . S 5 HOH D 3 603 112 HOH HOH . S 5 HOH D 4 604 20 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 . . . K 4 23.888 18.548 124.847 1 87.54 ? N DSH 503 B 1 HETATM 2 N N1 DSH . . . K 4 21.653 27.487 114.047 1 71.12 ? N1 DSH 503 B 1 HETATM 3 C C2 DSH . . . K 4 22.092 26.323 113.557 1 68.16 ? C2 DSH 503 B 1 HETATM 4 N N3 DSH . . . K 4 22.718 25.327 114.191 1 65.16 ? N3 DSH 503 B 1 HETATM 5 C C4 DSH . . . K 4 22.893 25.618 115.486 1 65.94 ? C4 DSH 503 B 1 HETATM 6 C C5 DSH . . . K 4 22.499 26.778 116.134 1 66.57 ? C5 DSH 503 B 1 HETATM 7 C C6 DSH . . . K 4 21.844 27.752 115.358 1 69.34 ? C6 DSH 503 B 1 HETATM 8 N N6 DSH . . . K 4 21.396 28.914 115.844 1 65.82 ? N6 DSH 503 B 1 HETATM 9 N N7 DSH . . . K 4 22.849 26.731 117.476 1 65.82 ? N7 DSH 503 B 1 HETATM 10 C C8 DSH . . . K 4 23.432 25.565 117.605 1 67.15 ? C8 DSH 503 B 1 HETATM 11 N N9 DSH . . . K 4 23.491 24.837 116.445 1 70.08 ? N9 DSH 503 B 1 HETATM 12 C CA DSH . . . K 4 23.208 19.119 123.657 1 85.66 ? CA DSH 503 B 1 HETATM 13 C CB DSH . . . K 4 24.2 19.573 122.613 1 82.62 ? CB DSH 503 B 1 HETATM 14 S SD DSH . . . K 4 24.054 20.054 119.842 1 78.64 ? SD DSH 503 B 1 HETATM 15 C CG DSH . . . K 4 23.492 20.372 121.539 1 80.74 ? CG DSH 503 B 1 HETATM 16 C C1' DSH . . . K 4 24.049 23.499 116.274 1 73.09 ? C1' DSH 503 B 1 HETATM 17 C C2' DSH . . . K 4 25.454 23.322 116.847 1 71.36 ? C2' DSH 503 B 1 HETATM 18 O O2' DSH . . . K 4 26.435 23.692 115.885 1 66.67 ? O2' DSH 503 B 1 HETATM 19 C C3' DSH . . . K 4 25.467 21.819 117.13 1 72.59 ? C3' DSH 503 B 1 HETATM 20 O O3' DSH . . . K 4 25.78 21.068 115.963 1 70.95 ? O3' DSH 503 B 1 HETATM 21 C C4' DSH . . . K 4 24.031 21.552 117.578 1 74.76 ? C4' DSH 503 B 1 HETATM 22 O O4' DSH . . . K 4 23.222 22.577 116.959 1 69.35 ? O4' DSH 503 B 1 HETATM 23 C C5' DSH . . . K 4 23.911 21.693 119.083 1 76.52 ? C5' DSH 503 B 1 HETATM 24 H HN DSH . . . K 4 23.42 18.811 125.708 1 105.05 ? HN DSH 503 B 1 HETATM 25 H HNA DSH . . . K 4 23.9 17.534 124.805 1 105.05 ? HNA DSH 503 B 1 HETATM 26 H H2 DSH . . . K 4 21.907 26.179 112.493 1 81.79 ? H2 DSH 503 B 1 HETATM 27 H HN6 DSH . . . K 4 21.506 29.164 116.822 1 78.99 ? HN6 DSH 503 B 1 HETATM 28 H HN6A DSH . . . K 4 20.93 29.575 115.231 1 78.99 ? HN6A DSH 503 B 1 HETATM 29 H H8 DSH . . . K 4 23.834 25.206 118.551 1 80.58 ? H8 DSH 503 B 1 HETATM 30 H HA DSH . . . K 4 22.527 18.377 123.242 1 102.79 ? HA DSH 503 B 1 HETATM 31 H HB DSH . . . K 4 24.695 18.727 122.139 1 99.15 ? HB DSH 503 B 1 HETATM 32 H HG DSH . . . K 4 23.604 21.441 121.715 1 96.89 ? HG DSH 503 B 1 HETATM 33 H HGA DSH . . . K 4 22.419 20.194 121.589 1 96.89 ? HGA DSH 503 B 1 HETATM 34 H H1' DSH . . . K 4 24.012 23.236 115.218 1 87.71 ? H1' DSH 503 B 1 HETATM 35 H H2' DSH . . . K 4 25.599 23.889 117.766 1 85.63 ? H2' DSH 503 B 1 HETATM 36 H HO2' DSH . . . K 4 26.354 23.06 115.123 1 80.01 ? HO2' DSH 503 B 1 HETATM 37 H H3' DSH . . . K 4 26.182 21.568 117.911 1 87.1 ? H3' DSH 503 B 1 HETATM 38 H HO3' DSH . . . K 4 25.114 21.324 115.272 1 85.14 ? HO3' DSH 503 B 1 HETATM 39 H H4' DSH . . . K 4 23.616 20.612 117.217 1 89.71 ? H4' DSH 503 B 1 HETATM 40 H H5' DSH . . . K 4 22.945 22.107 119.368 1 91.82 ? H5' DSH 503 B 1 HETATM 41 H "H5'A" DSH . . . K 4 24.638 22.382 119.511 1 91.82 ? "H5'A" DSH 503 B 1 HETATM 42 H HAA DSH . . . K 4 22.567 19.946 123.959 1 102.79 ? HAA DSH 503 B 1 HETATM 43 H HBA DSH . . . K 4 24.988 20.188 123.044 1 99.15 ? HBA DSH 503 B 1 HETATM 44 H H21 DSH . . . K 4 24.849 18.871 124.91 1 105.05 ? H21 DSH 503 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 67 _model_server_stats.create_model_time_ms 159 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 44 #