data_8THD # _model_server_result.job_id B1E2MLZ6INz057FqcRaYaw _model_server_result.datetime_utc '2025-02-20 18:17:27' _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 8thd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":401}' # _entry.id 8THD # _exptl.entry_id 8THD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 8THD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8THD _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 I N N ? 7 J N N ? 7 L N N ? 7 N N 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 metalc ? metalc1 B OG1 THR 56 B THR 56 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc2 J O1B AGS . B AGS 401 1_555 K MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc3 C OG1 THR 60 C THR 60 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc4 D OD2 ASP 140 D ASP 140 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 N O2G AGS . D AGS 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc6 N O2B AGS . D AGS 401 1_555 O MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 45 n n PG O2G AGS sing 46 n n PG O3G AGS sing 47 n n PG O3B AGS sing 48 n n PB O1B AGS doub 49 n n PB O2B AGS sing 50 n n PB O3B AGS sing 51 n n PB O3A AGS sing 52 n n PA O1A AGS doub 53 n n PA O2A AGS sing 54 n n PA O3A AGS sing 55 n n PA O5' AGS sing 56 n n O5' C5' AGS sing 57 n n C5' C4' AGS sing 58 n n C4' O4' AGS sing 59 n n C4' C3' AGS sing 60 n n O4' C1' AGS sing 61 n n C3' O3' AGS sing 62 n n C3' C2' AGS sing 63 n n C2' O2' AGS sing 64 n n C2' C1' AGS sing 65 n n C1' N9 AGS sing 66 n n N9 C8 AGS sing 67 n y N9 C4 AGS sing 68 n y C8 N7 AGS doub 69 n y N7 C5 AGS sing 70 n y C5 C6 AGS sing 71 n y C5 C4 AGS doub 72 n y C6 N6 AGS sing 73 n n C6 N1 AGS doub 74 n y N1 C2 AGS sing 75 n y C2 N3 AGS doub 76 n y N3 C4 AGS sing 77 n y O2G HOG2 AGS sing 78 n n O3G H21 AGS sing 79 n n O2B HOB2 AGS sing 80 n n O2A HOA2 AGS sing 81 n n C5' "H5'1" AGS sing 82 n n C5' "H5'2" AGS sing 83 n n C4' H4' AGS sing 84 n n C3' H3' AGS sing 85 n n O3' HO3' AGS sing 86 n n C2' H2' AGS sing 87 n n O2' HO2' AGS sing 88 n n C1' H1' AGS sing 89 n n C8 H8 AGS sing 90 n n N6 HN61 AGS sing 91 n n N6 HN62 AGS sing 92 n n C2 H2 AGS sing 93 n n # _atom_sites.entry_id 8THD _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 # 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 I 7 AGS A 1 801 801 AGS AGS . J 7 AGS B 1 401 401 AGS AGS . K 8 MG B 1 402 405 MG MG . L 7 AGS C 1 401 401 AGS AGS . M 8 MG C 1 402 402 MG MG . N 7 AGS D 1 401 401 AGS AGS . O 8 MG D 1 402 405 MG MG . P 9 ADP E 1 401 401 ADP ADP . # 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 PG AGS . . . L 7 158.674 188.437 167.544 1 60.32 ? PG AGS 401 C 1 HETATM 2 S S1G AGS . . . L 7 158.952 189.584 169.096 1 77.44 ? S1G AGS 401 C 1 HETATM 3 O O2G AGS . . . L 7 159.074 186.978 167.911 1 66.26 ? O2G AGS 401 C 1 HETATM 4 O O3G AGS . . . L 7 159.586 188.932 166.383 1 69.22 ? O3G AGS 401 C 1 HETATM 5 P PB AGS . . . L 7 156.047 189.245 167.84 1 54.99 ? PB AGS 401 C 1 HETATM 6 O O1B AGS . . . L 7 155.91 188.757 169.231 1 68.8 ? O1B AGS 401 C 1 HETATM 7 O O2B AGS . . . L 7 154.767 189.023 167.03 1 66.8 ? O2B AGS 401 C 1 HETATM 8 O O3B AGS . . . L 7 157.187 188.455 167.067 1 62.76 ? O3B AGS 401 C 1 HETATM 9 P PA AGS . . . L 7 155.542 191.779 168.787 1 65.46 ? PA AGS 401 C 1 HETATM 10 O O1A AGS . . . L 7 156.324 192.022 170.02 1 79.91 ? O1A AGS 401 C 1 HETATM 11 O O2A AGS . . . L 7 154.163 191.156 169.025 1 65.01 ? O2A AGS 401 C 1 HETATM 12 O O3A AGS . . . L 7 156.318 190.808 167.801 1 62.93 ? O3A AGS 401 C 1 HETATM 13 O O5' AGS . . . L 7 155.432 193.146 167.998 1 59.99 ? O5' AGS 401 C 1 HETATM 14 C C5' AGS . . . L 7 155.082 193.148 166.601 1 66.89 ? C5' AGS 401 C 1 HETATM 15 C C4' AGS . . . L 7 154.88 194.568 166.133 1 65.59 ? C4' AGS 401 C 1 HETATM 16 O O4' AGS . . . L 7 153.901 194.588 165.077 1 69.86 ? O4' AGS 401 C 1 HETATM 17 C C3' AGS . . . L 7 154.346 195.537 167.18 1 60.93 ? C3' AGS 401 C 1 HETATM 18 O O3' AGS . . . L 7 154.734 196.873 166.882 1 69.53 ? O3' AGS 401 C 1 HETATM 19 C C2' AGS . . . L 7 152.831 195.352 167.067 1 61.56 ? C2' AGS 401 C 1 HETATM 20 O O2' AGS . . . L 7 152.14 196.562 167.354 1 65.37 ? O2' AGS 401 C 1 HETATM 21 C C1' AGS . . . L 7 152.641 194.979 165.59 1 63.99 ? C1' AGS 401 C 1 HETATM 22 N N9 AGS . . . L 7 151.7 193.885 165.376 1 66.9 ? N9 AGS 401 C 1 HETATM 23 C C8 AGS . . . L 7 152.004 192.579 165.094 1 69.31 ? C8 AGS 401 C 1 HETATM 24 N N7 AGS . . . L 7 150.956 191.804 164.954 1 66.1 ? N7 AGS 401 C 1 HETATM 25 C C5 AGS . . . L 7 149.885 192.66 165.163 1 58.8 ? C5 AGS 401 C 1 HETATM 26 C C6 AGS . . . L 7 148.492 192.456 165.154 1 61.36 ? C6 AGS 401 C 1 HETATM 27 N N6 AGS . . . L 7 147.917 191.275 164.917 1 68.79 ? N6 AGS 401 C 1 HETATM 28 N N1 AGS . . . L 7 147.7 193.523 165.401 1 66.83 ? N1 AGS 401 C 1 HETATM 29 C C2 AGS . . . L 7 148.272 194.707 165.639 1 66.71 ? C2 AGS 401 C 1 HETATM 30 N N3 AGS . . . L 7 149.57 195.02 165.674 1 64.37 ? N3 AGS 401 C 1 HETATM 31 C C4 AGS . . . L 7 150.329 193.945 165.426 1 61.66 ? C4 AGS 401 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #