data_7TIB # _model_server_result.job_id mrK1mNUWPloucZg-z40OxQ _model_server_result.datetime_utc '2024-11-05 04:42:44' _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 7tib # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 7TIB # _exptl.entry_id 7TIB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 9 _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 7TIB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TIB _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _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,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 ? _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 ? 9 K N N ? 9 M N N ? 9 O N N ? 9 Q 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 OG1 THR 359 A THR 360 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc2 K O3G AGS . A AGS 901 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 K O1B AGS . A AGS 901 1_555 L MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 B OG1 THR 56 B THR 56 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc5 M O3G AGS . B AGS 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc6 M O1B AGS . B AGS 401 1_555 N MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc7 C OG1 THR 60 C THR 60 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc8 O O3G AGS . C AGS 401 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc9 O O1B AGS . C AGS 401 1_555 P MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc10 D OG1 THR 72 D THR 72 1_555 R MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc11 Q O3G AGS . D AGS 401 1_555 R MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc12 Q O2B AGS . D AGS 401 1_555 R MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? hydrog WATSON-CRICK hydrog1 I N1 DA 12 I DA 12 1_555 J N3 DT 19 J DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 I N6 DA 12 I DA 12 1_555 J O4 DT 19 J DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 I N1 DG 14 I DG 14 1_555 J N3 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 I N2 DG 14 I DG 14 1_555 J O2 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 I O6 DG 14 I DG 14 1_555 J N4 DC 17 J DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 I N3 DT 15 I DT 15 1_555 J N1 DA 16 J DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 I O4 DT 15 I DT 15 1_555 J N6 DA 16 J DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 I N1 DA 16 I DA 16 1_555 J N3 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 I N6 DA 16 I DA 16 1_555 J O4 DT 15 J DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 I N3 DC 17 I DC 17 1_555 J N1 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 I N4 DC 17 I DC 17 1_555 J O6 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 I O2 DC 17 I DC 17 1_555 J N2 DG 14 J DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 I N3 DT 18 I DT 18 1_555 J N1 DA 13 J DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I O4 DT 18 I DT 18 1_555 J N6 DA 13 J DA 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog15 I O2 DC 19 I DC 19 1_555 J N2 DG 12 J DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 I N1 DG 20 I DG 20 1_555 J N3 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I N2 DG 20 I DG 20 1_555 J O2 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I O6 DG 20 I DG 20 1_555 J N4 DC 11 J DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog19 I N1 DA 22 I DA 22 1_555 J N3 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog20 I N2 DG 23 I DG 23 1_555 J O2 DT 9 J DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DA MISPAIR' hydrog21 I N2 DG 25 I DG 25 1_555 J N1 DA 7 J DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 I N3 DC 27 I DC 27 1_555 J N1 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 I N4 DC 27 I DC 27 1_555 J O6 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 I O2 DC 27 I DC 27 1_555 J N2 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog25 I O4 DT 28 I DT 28 1_555 J N6 DA 3 J DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DG MISPAIR' hydrog26 I O4 DT 28 I DT 28 1_555 J N2 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 7TIB _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 K 9 AGS A 1 901 801 AGS AGS . L 10 MG A 1 902 811 MG MG . M 9 AGS B 1 401 802 AGS AGS . N 10 MG B 1 402 812 MG MG . O 9 AGS C 1 401 803 AGS AGS . P 10 MG C 1 402 813 MG MG . Q 9 AGS D 1 401 804 AGS AGS . R 10 MG D 1 402 814 MG MG . S 11 ADP E 1 401 805 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 . . . O 9 109.807 127.426 153.326 1 43.22 ? PG AGS 401 C 1 HETATM 2 S S1G AGS . . . O 9 111.702 127.174 152.951 1 43.22 ? S1G AGS 401 C 1 HETATM 3 O O2G AGS . . . O 9 108.978 126.348 152.568 1 43.22 ? O2G AGS 401 C 1 HETATM 4 O O3G AGS . . . O 9 109.372 128.841 152.843 1 43.22 ? O3G AGS 401 C 1 HETATM 5 P PB AGS . . . O 9 109.218 128.596 155.715 1 43.22 ? PB AGS 401 C 1 HETATM 6 O O1B AGS . . . O 9 109.876 129.787 155.13 1 43.22 ? O1B AGS 401 C 1 HETATM 7 O O2B AGS . . . O 9 109.696 128.296 157.138 1 43.22 ? O2B AGS 401 C 1 HETATM 8 O O3B AGS . . . O 9 109.553 127.303 154.859 1 43.22 ? O3B AGS 401 C 1 HETATM 9 P PA AGS . . . O 9 107.063 130.276 155.966 1 43.22 ? PA AGS 401 C 1 HETATM 10 O O1A AGS . . . O 9 106.964 130.952 154.654 1 43.22 ? O1A AGS 401 C 1 HETATM 11 O O2A AGS . . . O 9 107.96 131.006 156.97 1 43.22 ? O2A AGS 401 C 1 HETATM 12 O O3A AGS . . . O 9 107.649 128.81 155.811 1 43.22 ? O3A AGS 401 C 1 HETATM 13 O O5' AGS . . . O 9 105.597 130.084 156.531 1 43.22 ? O5' AGS 401 C 1 HETATM 14 C C5' AGS . . . O 9 104.48 129.845 155.65 1 43.22 ? C5' AGS 401 C 1 HETATM 15 C C4' AGS . . . O 9 103.202 130.05 156.421 1 43.22 ? C4' AGS 401 C 1 HETATM 16 O O4' AGS . . . O 9 103.041 128.985 157.382 1 43.22 ? O4' AGS 401 C 1 HETATM 17 C C3' AGS . . . O 9 103.143 131.337 157.235 1 43.22 ? C3' AGS 401 C 1 HETATM 18 O O3' AGS . . . O 9 102.651 132.411 156.442 1 43.22 ? O3' AGS 401 C 1 HETATM 19 C C2' AGS . . . O 9 102.178 130.968 158.361 1 43.22 ? C2' AGS 401 C 1 HETATM 20 O O2' AGS . . . O 9 100.819 131.111 157.962 1 43.22 ? O2' AGS 401 C 1 HETATM 21 C C1' AGS . . . O 9 102.516 129.493 158.596 1 43.22 ? C1' AGS 401 C 1 HETATM 22 N N9 AGS . . . O 9 103.498 129.262 159.65 1 43.22 ? N9 AGS 401 C 1 HETATM 23 C C8 AGS . . . O 9 104.71 128.636 159.522 1 43.22 ? C8 AGS 401 C 1 HETATM 24 N N7 AGS . . . O 9 105.395 128.564 160.638 1 43.22 ? N7 AGS 401 C 1 HETATM 25 C C5 AGS . . . O 9 104.577 129.19 161.566 1 43.22 ? C5 AGS 401 C 1 HETATM 26 C C6 AGS . . . O 9 104.728 129.445 162.943 1 43.22 ? C6 AGS 401 C 1 HETATM 27 N N6 AGS . . . O 9 105.801 129.086 163.652 1 43.22 ? N6 AGS 401 C 1 HETATM 28 N N1 AGS . . . O 9 103.722 130.09 163.575 1 43.22 ? N1 AGS 401 C 1 HETATM 29 C C2 AGS . . . O 9 102.645 130.451 162.87 1 43.22 ? C2 AGS 401 C 1 HETATM 30 N N3 AGS . . . O 9 102.392 130.265 161.572 1 43.22 ? N3 AGS 401 C 1 HETATM 31 C C4 AGS . . . O 9 103.404 129.624 160.973 1 43.22 ? C4 AGS 401 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 31 #