data_8G2F # _model_server_result.job_id Lvs1jinvr15ybdY8KOZpeA _model_server_result.datetime_utc '2024-11-14 20:57:53' _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 8g2f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8G2F # _exptl.entry_id 8G2F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 472.564 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[3-(N'-benzylcarbamimidamido)propyl]-5'-thioadenosine" _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 8G2F _cell.length_a 70.733 _cell.length_b 70.733 _cell.length_c 175.262 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G2F _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _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 'C21 H28 N8 O3 S' _chem_comp.formula_weight 472.564 _chem_comp.id DVS _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[3-(N'-benzylcarbamimidamido)propyl]-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 C12 N4 DVS sing 83 n n C12 C11 DVS sing 84 n n N7 C DVS sing 85 n n N5 C14 DVS sing 86 n n N5 C13 DVS sing 87 n n N4 C13 DVS sing 88 n n C14 C15 DVS sing 89 n n C13 N6 DVS doub 90 n n C11 C10 DVS sing 91 n n N3 C1 DVS sing 92 n y N3 C4 DVS doub 93 n y C C1 DVS doub 94 n y C N1 DVS sing 95 n y C15 C16 DVS doub 96 n y C15 C20 DVS sing 97 n y C10 S DVS sing 98 n n C1 C2 DVS sing 99 n y C16 C17 DVS sing 100 n y C4 N2 DVS sing 101 n y N1 C3 DVS doub 102 n y S C9 DVS sing 103 n n C20 C19 DVS doub 104 n y C2 N2 DVS sing 105 n y C2 N DVS doub 106 n y C17 C18 DVS doub 107 n y N2 C5 DVS sing 108 n n C3 N DVS sing 109 n y O C5 DVS sing 110 n n O C8 DVS sing 111 n n C9 C8 DVS sing 112 n n C19 C18 DVS sing 113 n y C5 C6 DVS sing 114 n n C8 C7 DVS sing 115 n n C6 C7 DVS sing 116 n n C6 O2 DVS sing 117 n n C7 O1 DVS sing 118 n n C7 H1 DVS sing 119 n n C8 H2 DVS sing 120 n n C9 H3 DVS sing 121 n n C9 H4 DVS sing 122 n n O1 H5 DVS sing 123 n n C5 H6 DVS sing 124 n n C6 H7 DVS sing 125 n n C4 H8 DVS sing 126 n n C3 H9 DVS sing 127 n n N4 H10 DVS sing 128 n n O2 H11 DVS sing 129 n n N7 H12 DVS sing 130 n n N7 H13 DVS sing 131 n n C10 H14 DVS sing 132 n n C10 H15 DVS sing 133 n n C11 H16 DVS sing 134 n n C11 H17 DVS sing 135 n n C12 H18 DVS sing 136 n n C12 H19 DVS sing 137 n n N6 H20 DVS sing 138 n n N5 H21 DVS sing 139 n n C14 H22 DVS sing 140 n n C14 H23 DVS sing 141 n n C20 H24 DVS sing 142 n n C19 H25 DVS sing 143 n n C18 H26 DVS sing 144 n n C17 H27 DVS sing 145 n n C16 H28 DVS sing 146 n n # _atom_sites.entry_id 8G2F _atom_sites.fract_transf_matrix[1][1] 0.014138 _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] 0.014138 _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] 0.005706 _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 DVS A 1 601 601 DVS XXX . C 3 HOH A 1 701 41 HOH HOH . C 3 HOH A 2 702 16 HOH HOH . C 3 HOH A 3 703 31 HOH HOH . C 3 HOH A 4 704 19 HOH HOH . C 3 HOH A 5 705 38 HOH HOH . C 3 HOH A 6 706 36 HOH HOH . C 3 HOH A 7 707 22 HOH HOH . C 3 HOH A 8 708 28 HOH HOH . C 3 HOH A 9 709 39 HOH HOH . C 3 HOH A 10 710 1 HOH HOH . C 3 HOH A 11 711 5 HOH HOH . C 3 HOH A 12 712 17 HOH HOH . C 3 HOH A 13 713 8 HOH HOH . C 3 HOH A 14 714 37 HOH HOH . C 3 HOH A 15 715 4 HOH HOH . C 3 HOH A 16 716 30 HOH HOH . C 3 HOH A 17 717 25 HOH HOH . C 3 HOH A 18 718 9 HOH HOH . C 3 HOH A 19 719 11 HOH HOH . C 3 HOH A 20 720 15 HOH HOH . C 3 HOH A 21 721 40 HOH HOH . C 3 HOH A 22 722 35 HOH HOH . C 3 HOH A 23 723 23 HOH HOH . C 3 HOH A 24 724 20 HOH HOH . C 3 HOH A 25 725 3 HOH HOH . C 3 HOH A 26 726 27 HOH HOH . C 3 HOH A 27 727 13 HOH HOH . C 3 HOH A 28 728 21 HOH HOH . C 3 HOH A 29 729 12 HOH HOH . C 3 HOH A 30 730 2 HOH HOH . C 3 HOH A 31 731 14 HOH HOH . C 3 HOH A 32 732 18 HOH HOH . C 3 HOH A 33 733 34 HOH HOH . C 3 HOH A 34 734 42 HOH HOH . C 3 HOH A 35 735 32 HOH HOH . C 3 HOH A 36 736 29 HOH HOH . C 3 HOH A 37 737 7 HOH HOH . C 3 HOH A 38 738 10 HOH HOH . C 3 HOH A 39 739 6 HOH HOH . C 3 HOH A 40 740 33 HOH HOH . C 3 HOH A 41 741 24 HOH HOH . C 3 HOH A 42 742 26 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 N1 DVS . . . B 2 27.172 1.098 -3.994 1 71.19 ? N1 DVS 601 A 1 HETATM 2 C C7 DVS . . . B 2 20.682 -0.773 -0.682 1 66.81 ? C7 DVS 601 A 1 HETATM 3 C C8 DVS . . . B 2 20.893 -1.903 -1.713 1 65.89 ? C8 DVS 601 A 1 HETATM 4 N N2 DVS . . . B 2 23.338 0.372 -3.007 1 61.9 ? N2 DVS 601 A 1 HETATM 5 C C9 DVS . . . B 2 19.662 -2.21 -2.545 1 65.99 ? C9 DVS 601 A 1 HETATM 6 O O1 DVS . . . B 2 21.011 -1.221 0.631 1 62.87 ? O1 DVS 601 A 1 HETATM 7 C C1 DVS . . . B 2 24.839 1.283 -4.34 1 59.73 ? C1 DVS 601 A 1 HETATM 8 C C5 DVS . . . B 2 22.658 -0.409 -1.975 1 63.14 ? C5 DVS 601 A 1 HETATM 9 C C6 DVS . . . B 2 21.605 0.359 -1.176 1 60.92 ? C6 DVS 601 A 1 HETATM 10 N N3 DVS . . . B 2 23.599 1.636 -4.853 1 65.63 ? N3 DVS 601 A 1 HETATM 11 C C4 DVS . . . B 2 22.749 1.077 -4.025 1 65.42 ? C4 DVS 601 A 1 HETATM 12 C C3 DVS . . . B 2 26.88 0.381 -2.901 1 65.69 ? C3 DVS 601 A 1 HETATM 13 C C2 DVS . . . B 2 24.694 0.511 -3.195 1 62.84 ? C2 DVS 601 A 1 HETATM 14 N N4 DVS . . . B 2 16.288 -3.725 -5.816 1 60.85 ? N4 DVS 601 A 1 HETATM 15 O O2 DVS . . . B 2 22.186 1.034 -0.065 1 64.27 ? O2 DVS 601 A 1 HETATM 16 O O DVS . . . B 2 21.962 -1.48 -2.596 1 61.55 ? O DVS 601 A 1 HETATM 17 N N DVS . . . B 2 25.679 0.027 -2.428 1 62.02 ? N DVS 601 A 1 HETATM 18 C C DVS . . . B 2 26.156 1.568 -4.756 1 65.39 ? C DVS 601 A 1 HETATM 19 N N7 DVS . . . B 2 26.458 2.224 -5.88 1 66.2 ? N7 DVS 601 A 1 HETATM 20 S S DVS . . . B 2 19.056 -0.76 -3.441 1 70.87 ? S DVS 601 A 1 HETATM 21 C C10 DVS . . . B 2 17.678 -1.469 -4.392 1 76.1 ? C10 DVS 601 A 1 HETATM 22 C C11 DVS . . . B 2 18.153 -2.134 -5.668 1 70.79 ? C11 DVS 601 A 1 HETATM 23 C C12 DVS . . . B 2 17.022 -2.67 -6.501 1 63.54 ? C12 DVS 601 A 1 HETATM 24 C C13 DVS . . . B 2 14.96 -3.717 -5.714 1 55.52 ? C13 DVS 601 A 1 HETATM 25 N N6 DVS . . . B 2 14.261 -4.775 -5.478 1 61.75 ? N6 DVS 601 A 1 HETATM 26 N N5 DVS . . . B 2 14.302 -2.521 -5.825 1 52.91 ? N5 DVS 601 A 1 HETATM 27 C C14 DVS . . . B 2 12.854 -2.403 -5.795 1 54.5 ? C14 DVS 601 A 1 HETATM 28 C C15 DVS . . . B 2 12.283 -2.135 -4.422 1 61.15 ? C15 DVS 601 A 1 HETATM 29 C C20 DVS . . . B 2 12.983 -2.471 -3.271 1 60.13 ? C20 DVS 601 A 1 HETATM 30 C C19 DVS . . . B 2 12.4 -2.322 -2.016 1 58.97 ? C19 DVS 601 A 1 HETATM 31 C C18 DVS . . . B 2 11.127 -1.822 -1.898 1 60.78 ? C18 DVS 601 A 1 HETATM 32 C C17 DVS . . . B 2 10.422 -1.469 -3.035 1 70.01 ? C17 DVS 601 A 1 HETATM 33 C C16 DVS . . . B 2 10.995 -1.625 -4.287 1 63.98 ? C16 DVS 601 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 33 #