data_5DNY # _model_server_result.job_id JRjUfgz6OHAIyWDKqsZYGg _model_server_result.datetime_utc '2025-03-22 16:11:57' _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 5dny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1101}' # _entry.id 5DNY # _exptl.entry_id 5DNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 6 _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 5DNY _cell.length_a 84.303 _cell.length_b 130.111 _cell.length_c 166.656 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M,N _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 ? 6 I N N ? 6 L 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 OD2 ASP 28 A ASP 8 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc2 A OD2 ASP 69 A ASP 49 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc3 A OD2 ASP 69 A ASP 49 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc4 C OD2 ASP 28 C ASP 8 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc5 C OD2 ASP 69 C ASP 49 1_555 J MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc6 C OD2 ASP 69 C ASP 49 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? hydrog WATSON-CRICK hydrog1 E N1 DG 4 E DG 4 1_555 F N3 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N2 DG 4 E DG 4 1_555 F O2 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E O6 DG 4 E DG 4 1_555 F N4 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N3 DT 5 E DT 5 1_555 F N1 DA 25 F DA -5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E O4 DT 5 E DT 5 1_555 F N6 DA 25 F DA -5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog6 E O4 DT 6 E DT 6 1_555 F N4 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N3 DT 6 E DT 6 1_555 F N1 DA 24 F DA -6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E O4 DT 6 E DT 6 1_555 F N6 DA 24 F DA -6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog9 E O6 DG 7 E DG 7 1_555 F N4 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N1 DG 7 E DG 7 1_555 F N3 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N2 DG 7 E DG 7 1_555 F O2 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E O6 DG 7 E DG 7 1_555 F N4 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E N1 DG 8 E DG 8 1_555 F N3 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N2 DG 8 E DG 8 1_555 F O2 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E O6 DG 8 E DG 8 1_555 F N4 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E N1 DG 9 E DG 9 1_555 F N3 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N2 DG 9 E DG 9 1_555 F O2 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E O6 DG 9 E DG 9 1_555 F N4 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog19 E N1 DA 10 E DA 10 1_555 F N3 DT 20 F DT -10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E N3 DT 11 E DT 11 1_555 F N1 DA 19 F DA -11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E O4 DT 11 E DT 11 1_555 F N6 DA 19 F DA -11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog22 E N3 DT 12 E DT 12 1_555 F N1 DA 18 F DA -12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog23 E N2 DG 13 E DG 13 1_555 F N3 DC 17 F DC -13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E N1 DA 14 E DA 14 1_555 F N3 DT 16 F DT -14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E N6 DA 14 E DA 14 1_555 F O4 DT 16 F DT -14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog26 E N2 DG 15 E DG 15 1_555 F O2 DC 15 F DC -15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog27 E N1 DA 16 E DA 16 1_555 F N3 DT 14 F DT -16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 E N3 DC 17 E DC 17 1_555 F N1 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 E N4 DC 17 E DC 17 1_555 F O6 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 E O2 DC 17 E DC 17 1_555 F N2 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog31 E N1 DA 18 E DA 18 1_555 F N3 DT 12 F DT -18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog32 E O2 DC 19 E DC 19 1_555 F N2 DG 11 F DG -19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 E N1 DA 20 E DA 20 1_555 F N3 DT 10 F DT -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 E N6 DA 20 E DA 20 1_555 F O4 DT 10 F DT -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog35 E N3 DC 21 E DC 21 1_555 F N2 DG 9 F DG -21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 E N1 DA 22 E DA 22 1_555 F N3 DT 8 F DT -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 E N6 DA 22 E DA 22 1_555 F O4 DT 8 F DT -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 E N3 DT 23 E DT 23 1_555 F N1 DA 7 F DA -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 E O4 DT 23 E DT 23 1_555 F N6 DA 7 F DA -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog40 E O2 DC 25 E DC 25 1_555 F N2 DG 5 F DG -25 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 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 5DNY _atom_sites.fract_transf_matrix[1][1] 0.011862 _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] 0.007686 _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] 0.006 _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 G 5 MG A 1 401 1 MG MG . H 5 MG A 1 402 1 MG MG . I 6 AGS B 1 1101 1006 AGS AGS . J 5 MG C 1 401 1 MG MG . K 5 MG C 1 402 1 MG MG . L 6 AGS D 1 1101 1006 AGS AGS . M 7 HOH A 1 501 2 HOH HOH . N 7 HOH C 1 501 1 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 P PG AGS . . . L 6 -2.727 12.751 -42.772 1 295.31 ? PG AGS 1101 D 1 HETATM 2 S S1G AGS . . . L 6 -4.216 11.769 -43.554 1 338.08 ? S1G AGS 1101 D 1 HETATM 3 O O2G AGS . . . L 6 -1.462 11.842 -42.748 1 292.77 ? O2G AGS 1101 D 1 HETATM 4 O O3G AGS . . . L 6 -3.073 13.173 -41.313 1 294.59 ? O3G AGS 1101 D 1 HETATM 5 P PB AGS . . . L 6 -1.174 14.868 -43.175 1 240.32 ? PB AGS 1101 D 1 HETATM 6 O O1B AGS . . . L 6 -1.441 16.323 -43.249 1 240.48 ? O1B AGS 1101 D 1 HETATM 7 O O2B AGS . . . L 6 -0.812 14.379 -41.772 1 237.82 ? O2B AGS 1101 D 1 HETATM 8 O O3B AGS . . . L 6 -2.429 14.025 -43.608 1 265.96 ? O3B AGS 1101 D 1 HETATM 9 P PA AGS . . . L 6 1.33 13.859 -43.398 1 110.26 ? PA AGS 1101 D 1 HETATM 10 O O1A AGS . . . L 6 1.209 12.336 -43.488 1 111.33 ? O1A AGS 1101 D 1 HETATM 11 O O2A AGS . . . L 6 1.531 14.399 -42.035 1 110.62 ? O2A AGS 1101 D 1 HETATM 12 O O3A AGS . . . L 6 0.037 14.45 -44.081 1 229.92 ? O3A AGS 1101 D 1 HETATM 13 O O5' AGS . . . L 6 2.452 14.417 -44.333 1 51.07 ? O5' AGS 1101 D 1 HETATM 14 C C5' AGS . . . L 6 2.781 13.66 -45.494 1 59.67 ? C5' AGS 1101 D 1 HETATM 15 C C4' AGS . . . L 6 3.306 14.571 -46.572 1 62.44 ? C4' AGS 1101 D 1 HETATM 16 O O4' AGS . . . L 6 4.75 14.519 -46.574 1 67.24 ? O4' AGS 1101 D 1 HETATM 17 C C3' AGS . . . L 6 2.843 14.158 -47.971 1 54.81 ? C3' AGS 1101 D 1 HETATM 18 O O3' AGS . . . L 6 2.432 15.294 -48.722 1 50.33 ? O3' AGS 1101 D 1 HETATM 19 C C2' AGS . . . L 6 4.078 13.487 -48.579 1 67.84 ? C2' AGS 1101 D 1 HETATM 20 O O2' AGS . . . L 6 4.13 13.69 -49.986 1 75.51 ? O2' AGS 1101 D 1 HETATM 21 C C1' AGS . . . L 6 5.213 14.227 -47.876 1 71.75 ? C1' AGS 1101 D 1 HETATM 22 N N9 AGS . . . L 6 6.452 13.464 -47.76 1 75.84 ? N9 AGS 1101 D 1 HETATM 23 C C8 AGS . . . L 6 6.595 12.168 -47.335 1 69.17 ? C8 AGS 1101 D 1 HETATM 24 N N7 AGS . . . L 6 7.831 11.731 -47.35 1 59.82 ? N7 AGS 1101 D 1 HETATM 25 C C5 AGS . . . L 6 8.551 12.805 -47.859 1 62.46 ? C5 AGS 1101 D 1 HETATM 26 C C6 AGS . . . L 6 9.92 12.982 -48.134 1 57.94 ? C6 AGS 1101 D 1 HETATM 27 N N6 AGS . . . L 6 10.848 12.046 -47.93 1 57.61 ? N6 AGS 1101 D 1 HETATM 28 N N1 AGS . . . L 6 10.308 14.176 -48.638 1 59.99 ? N1 AGS 1101 D 1 HETATM 29 C C2 AGS . . . L 6 9.384 15.118 -48.845 1 81.34 ? C2 AGS 1101 D 1 HETATM 30 N N3 AGS . . . L 6 8.068 15.066 -48.622 1 91.24 ? N3 AGS 1101 D 1 HETATM 31 C C4 AGS . . . L 6 7.712 13.871 -48.125 1 78.44 ? C4 AGS 1101 D 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #