data_7XXH # _model_server_result.job_id Qy3-vEEKEzC3IE_KnyUQrQ _model_server_result.datetime_utc '2024-12-26 10:07:54' _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 7xxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 7XXH # _exptl.entry_id 7XXH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 473.293 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-(methylsulfanyl)adenosine 5'-(trihydrogen 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 7XXH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XXH _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 # _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 ? _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 6 _struct_asym.id F _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 disulf ? disulf1 A SG CYS 44 R CYS 42 1_555 A SG CYS 298 R CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 126 R CYS 124 1_555 A SG CYS 204 R CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 E SG CYS 22 H CYS 22 1_555 E SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 E SG CYS 159 H CYS 159 1_555 E SG CYS 229 H CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _chem_comp.formula 'C11 H17 N5 O10 P2 S' _chem_comp.formula_weight 473.293 _chem_comp.id 6AD _chem_comp.mon_nstd_flag . _chem_comp.name "2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2-methylthio-adenosine-5'-diphosphate" # 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 C11 S1 6AD sing 1 n n S1 C2 6AD sing 2 n n N1 C2 6AD doub 3 n y N1 C6 6AD sing 4 n y C2 N3 6AD sing 5 n y N6 C6 6AD sing 6 n n C6 C5 6AD doub 7 n y N3 C4 6AD doub 8 n y C5 C4 6AD sing 9 n y C5 N7 6AD sing 10 n y C4 N9 6AD sing 11 n y N7 C8 6AD doub 12 n y N9 C8 6AD sing 13 n y N9 C1' 6AD sing 14 n n O4' C1' 6AD sing 15 n n O4' C4' 6AD sing 16 n n C1' C2' 6AD sing 17 n n C4' C5' 6AD sing 18 n n C4' C3' 6AD sing 19 n n O1A PA 6AD doub 20 n n C2' O2' 6AD sing 21 n n C2' C3' 6AD sing 22 n n C5' O5' 6AD sing 23 n n O3' C3' 6AD sing 24 n n O5' PA 6AD sing 25 n n PA O2A 6AD sing 26 n n PA O3A 6AD sing 27 n n O1B PB 6AD doub 28 n n O3A PB 6AD sing 29 n n O3B PB 6AD sing 30 n n PB O2B 6AD sing 31 n n O2B H1 6AD sing 32 n n O3B H2 6AD sing 33 n n O2A H3 6AD sing 34 n n C5' H4 6AD sing 35 n n C5' H5 6AD sing 36 n n C4' H6 6AD sing 37 n n C3' H7 6AD sing 38 n n O3' H8 6AD sing 39 n n C2' H9 6AD sing 40 n n O2' H10 6AD sing 41 n n C1' H11 6AD sing 42 n n C8 H12 6AD sing 43 n n C11 H13 6AD sing 44 n n C11 H14 6AD sing 45 n n C11 H15 6AD sing 46 n n N6 H16 6AD sing 47 n n N6 H17 6AD sing 48 n n # _atom_sites.entry_id 7XXH _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id 6AD _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id 6AD _pdbx_nonpoly_scheme.auth_mon_id LIG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 O O2B 6AD . . . F 6 153.877 110.886 148.777 1 72.45 ? O2B 6AD 501 R 1 HETATM 2 P PB 6AD . . . F 6 153.541 111.265 147.363 1 72.45 ? PB 6AD 501 R 1 HETATM 3 O O3B 6AD . . . F 6 152.153 111.806 147.301 1 72.45 ? O3B 6AD 501 R 1 HETATM 4 O O1B 6AD . . . F 6 153.642 110.044 146.48 1 72.45 ? O1B 6AD 501 R 1 HETATM 5 O O3A 6AD . . . F 6 154.614 112.413 146.818 1 72.45 ? O3A 6AD 501 R 1 HETATM 6 P PA 6AD . . . F 6 154.763 112.791 145.191 1 72.45 ? PA 6AD 501 R 1 HETATM 7 O O2A 6AD . . . F 6 155.781 113.881 145.006 1 72.45 ? O2A 6AD 501 R 1 HETATM 8 O O1A 6AD . . . F 6 153.43 113.225 144.673 1 72.45 ? O1A 6AD 501 R 1 HETATM 9 O O5' 6AD . . . F 6 155.246 111.458 144.353 1 72.45 ? O5' 6AD 501 R 1 HETATM 10 C C5' 6AD . . . F 6 155.629 111.642 143.013 1 72.45 ? C5' 6AD 501 R 1 HETATM 11 C C4' 6AD . . . F 6 157.186 111.672 142.945 1 72.45 ? C4' 6AD 501 R 1 HETATM 12 O O4' 6AD . . . F 6 157.685 112.026 144.106 1 72.45 ? O4' 6AD 501 R 1 HETATM 13 C C3' 6AD . . . F 6 157.751 110.233 142.632 1 72.45 ? C3' 6AD 501 R 1 HETATM 14 O O3' 6AD . . . F 6 158.071 110.13 141.277 1 72.45 ? O3' 6AD 501 R 1 HETATM 15 C C2' 6AD . . . F 6 159.011 110.11 143.474 1 72.45 ? C2' 6AD 501 R 1 HETATM 16 O O2' 6AD . . . F 6 160.105 110.476 142.75 1 72.45 ? O2' 6AD 501 R 1 HETATM 17 C C1' 6AD . . . F 6 158.842 110.972 144.498 1 72.45 ? C1' 6AD 501 R 1 HETATM 18 N N9 6AD . . . F 6 158.318 110.651 145.868 1 72.45 ? N9 6AD 501 R 1 HETATM 19 C C8 6AD . . . F 6 157.098 110.253 146.18 1 72.45 ? C8 6AD 501 R 1 HETATM 20 N N7 6AD . . . F 6 157.013 110.073 147.519 1 72.45 ? N7 6AD 501 R 1 HETATM 21 C C5 6AD . . . F 6 158.213 110.368 148.048 1 72.45 ? C5 6AD 501 R 1 HETATM 22 C C4 6AD . . . F 6 159.058 110.741 147.005 1 72.45 ? C4 6AD 501 R 1 HETATM 23 N N3 6AD . . . F 6 160.333 111.089 147.261 1 72.45 ? N3 6AD 501 R 1 HETATM 24 C C2 6AD . . . F 6 160.8 111.077 148.529 1 72.45 ? C2 6AD 501 R 1 HETATM 25 S S1 6AD . . . F 6 162.555 111.56 148.842 1 72.45 ? S1 6AD 501 R 1 HETATM 26 C C11 6AD . . . F 6 163.653 110.494 147.847 1 72.45 ? C11 6AD 501 R 1 HETATM 27 N N1 6AD . . . F 6 160.031 110.729 149.537 1 72.45 ? N1 6AD 501 R 1 HETATM 28 C C6 6AD . . . F 6 158.733 110.366 149.359 1 72.45 ? C6 6AD 501 R 1 HETATM 29 N N6 6AD . . . F 6 157.898 109.984 150.493 1 72.45 ? N6 6AD 501 R 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 29 #