data_8RZ9 # _model_server_result.job_id HTGOXVhLJHyfSOH8E_v8vg _model_server_result.datetime_utc '2025-02-28 06:56:50' _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 8rz9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 8RZ9 # _exptl.entry_id 8RZ9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 8RZ9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RZ9 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 D N N ? 4 F 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 A OG SER 676 A SER 676 1_555 C MG MG . A MG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? metalc ? metalc2 A OD1 ASP 748 A ASP 748 1_555 C MG MG . A MG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc3 C MG MG . A MG 2000 1_555 D O2G AGS . A AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc4 C MG MG . A MG 2000 1_555 D O2B AGS . A AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc5 B OG SER 903 B SER 903 1_555 E MG MG . B MG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc6 E MG MG . B MG 2000 1_555 F O2B AGS . B AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc7 E MG MG . B MG 2000 1_555 F O2G AGS . B AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _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 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 8RZ9 _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 C 3 MG A 1 2000 2000 MG MG . D 4 AGS A 1 2001 2001 AGS AGS . E 3 MG B 1 2000 2000 MG MG . F 4 AGS B 1 2001 2001 AGS AGS . # 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 . . . D 4 155.609 155.838 120.711 1 55.9 ? PG AGS 2001 A 1 HETATM 2 S S1G AGS . . . D 4 156.335 154.065 120.605 1 62.42 ? S1G AGS 2001 A 1 HETATM 3 O O2G AGS . . . D 4 154.333 155.956 121.512 1 50.95 ? O2G AGS 2001 A 1 HETATM 4 O O3G AGS . . . D 4 155.364 156.487 119.364 1 66.69 ? O3G AGS 2001 A 1 HETATM 5 P PB AGS . . . D 4 156.209 157.962 122.392 1 68.27 ? PB AGS 2001 A 1 HETATM 6 O O1B AGS . . . D 4 156.089 159.202 121.594 1 70.24 ? O1B AGS 2001 A 1 HETATM 7 O O2B AGS . . . D 4 154.994 157.476 123.113 1 61.36 ? O2B AGS 2001 A 1 HETATM 8 O O3B AGS . . . D 4 156.7 156.766 121.453 1 59.78 ? O3B AGS 2001 A 1 HETATM 9 P PA AGS . . . D 4 156.904 158.158 125.026 1 80.91 ? PA AGS 2001 A 1 HETATM 10 O O1A AGS . . . D 4 156.217 156.88 125.373 1 84.75 ? O1A AGS 2001 A 1 HETATM 11 O O2A AGS . . . D 4 156.137 159.422 125.253 1 82.23 ? O2A AGS 2001 A 1 HETATM 12 O O3A AGS . . . D 4 157.349 158.134 123.49 1 73.37 ? O3A AGS 2001 A 1 HETATM 13 O O5' AGS . . . D 4 158.32 158.199 125.765 1 73.72 ? O5' AGS 2001 A 1 HETATM 14 C C5' AGS . . . D 4 159.1 156.981 125.807 1 72.5 ? C5' AGS 2001 A 1 HETATM 15 C C4' AGS . . . D 4 160.402 157.269 126.503 1 77.27 ? C4' AGS 2001 A 1 HETATM 16 O O4' AGS . . . D 4 160.974 158.474 125.939 1 74.89 ? O4' AGS 2001 A 1 HETATM 17 C C3' AGS . . . D 4 160.312 157.573 128.003 1 84 ? C3' AGS 2001 A 1 HETATM 18 O O3' AGS . . . D 4 160.308 156.391 128.791 1 91.54 ? O3' AGS 2001 A 1 HETATM 19 C C2' AGS . . . D 4 161.582 158.4 128.225 1 81.14 ? C2' AGS 2001 A 1 HETATM 20 O O2' AGS . . . D 4 162.739 157.603 128.367 1 80.85 ? O2' AGS 2001 A 1 HETATM 21 C C1' AGS . . . D 4 161.634 159.22 126.938 1 73.31 ? C1' AGS 2001 A 1 HETATM 22 N N9 AGS . . . D 4 161.008 160.536 127.033 1 59.15 ? N9 AGS 2001 A 1 HETATM 23 C C8 AGS . . . D 4 159.682 160.82 126.868 1 50.81 ? C8 AGS 2001 A 1 HETATM 24 N N7 AGS . . . D 4 159.401 162.086 126.99 1 50.81 ? N7 AGS 2001 A 1 HETATM 25 C C5 AGS . . . D 4 160.614 162.682 127.27 1 49.38 ? C5 AGS 2001 A 1 HETATM 26 C C6 AGS . . . D 4 160.974 164.02 127.523 1 53.04 ? C6 AGS 2001 A 1 HETATM 27 N N6 AGS . . . D 4 160.115 165.035 127.529 1 48.79 ? N6 AGS 2001 A 1 HETATM 28 N N1 AGS . . . D 4 162.281 164.272 127.776 1 61.85 ? N1 AGS 2001 A 1 HETATM 29 C C2 AGS . . . D 4 163.149 163.248 127.78 1 69.6 ? C2 AGS 2001 A 1 HETATM 30 N N3 AGS . . . D 4 162.919 161.958 127.544 1 65.32 ? N3 AGS 2001 A 1 HETATM 31 C C4 AGS . . . D 4 161.616 161.735 127.299 1 54.34 ? C4 AGS 2001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #