data_5DNY # _model_server_result.job_id VEGn_trKq9-3jQfeFBeuug _model_server_result.datetime_utc '2024-11-05 00:55:38' _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":"I","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 . . . I 6 -21.367 1.454 -42.165 1 180.14 ? PG AGS 1101 B 1 HETATM 2 S S1G AGS . . . I 6 -21.073 3.081 -41.135 1 186.04 ? S1G AGS 1101 B 1 HETATM 3 O O2G AGS . . . I 6 -21.008 0.207 -41.305 1 172.47 ? O2G AGS 1101 B 1 HETATM 4 O O3G AGS . . . I 6 -20.464 1.474 -43.433 1 161.92 ? O3G AGS 1101 B 1 HETATM 5 P PB AGS . . . I 6 -24.012 1.17 -41.546 1 116.35 ? PB AGS 1101 B 1 HETATM 6 O O1B AGS . . . I 6 -25.139 2.123 -41.941 1 29.6 ? O1B AGS 1101 B 1 HETATM 7 O O2B AGS . . . I 6 -23.527 1.463 -40.185 1 111.34 ? O2B AGS 1101 B 1 HETATM 8 O O3B AGS . . . I 6 -22.857 1.368 -42.612 1 215.78 ? O3B AGS 1101 B 1 HETATM 9 P PA AGS . . . I 6 -24.12 -1.481 -40.727 1 155.75 ? PA AGS 1101 B 1 HETATM 10 O O1A AGS . . . I 6 -24.463 -2.811 -41.298 1 170.79 ? O1A AGS 1101 B 1 HETATM 11 O O2A AGS . . . I 6 -22.632 -1.256 -40.44 1 170.39 ? O2A AGS 1101 B 1 HETATM 12 O O3A AGS . . . I 6 -24.597 -0.3 -41.686 1 174.38 ? O3A AGS 1101 B 1 HETATM 13 O O5' AGS . . . I 6 -25.034 -1.293 -39.454 1 50.37 ? O5' AGS 1101 B 1 HETATM 14 C C5' AGS . . . I 6 -26.128 -2.207 -39.261 1 32.96 ? C5' AGS 1101 B 1 HETATM 15 C C4' AGS . . . I 6 -26.568 -2.29 -37.819 1 43.07 ? C4' AGS 1101 B 1 HETATM 16 O O4' AGS . . . I 6 -27.106 -3.603 -37.556 1 66.94 ? O4' AGS 1101 B 1 HETATM 17 C C3' AGS . . . I 6 -25.534 -2.002 -36.726 1 47.49 ? C3' AGS 1101 B 1 HETATM 18 O O3' AGS . . . I 6 -26.011 -1.018 -35.814 1 86.44 ? O3' AGS 1101 B 1 HETATM 19 C C2' AGS . . . I 6 -25.333 -3.362 -36.044 1 54.44 ? C2' AGS 1101 B 1 HETATM 20 O O2' AGS . . . I 6 -25.114 -3.206 -34.645 1 52.43 ? O2' AGS 1101 B 1 HETATM 21 C C1' AGS . . . I 6 -26.675 -4.052 -36.291 1 68.74 ? C1' AGS 1101 B 1 HETATM 22 N N9 AGS . . . I 6 -26.59 -5.509 -36.338 1 63.33 ? N9 AGS 1101 B 1 HETATM 23 C C8 AGS . . . I 6 -25.576 -6.27 -36.857 1 56.5 ? C8 AGS 1101 B 1 HETATM 24 N N7 AGS . . . I 6 -25.795 -7.563 -36.798 1 65.16 ? N7 AGS 1101 B 1 HETATM 25 C C5 AGS . . . I 6 -27.066 -7.653 -36.253 1 80.18 ? C5 AGS 1101 B 1 HETATM 26 C C6 AGS . . . I 6 -27.889 -8.755 -35.941 1 87.14 ? C6 AGS 1101 B 1 HETATM 27 N N6 AGS . . . I 6 -27.538 -10.027 -36.143 1 86.48 ? N6 AGS 1101 B 1 HETATM 28 N N1 AGS . . . I 6 -29.104 -8.498 -35.407 1 91.59 ? N1 AGS 1101 B 1 HETATM 29 C C2 AGS . . . I 6 -29.462 -7.227 -35.201 1 89.26 ? C2 AGS 1101 B 1 HETATM 30 N N3 AGS . . . I 6 -28.773 -6.111 -35.454 1 86.5 ? N3 AGS 1101 B 1 HETATM 31 C C4 AGS . . . I 6 -27.577 -6.396 -35.981 1 78.48 ? C4 AGS 1101 B 1 # _model_server_stats.io_time_ms 140 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #