data_1RQQ # _model_server_result.job_id rOF7EtJoihDjfWVwlmr4ww _model_server_result.datetime_utc '2024-11-22 06:26:44' _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 1rqq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":117}' # _entry.id 1RQQ # _exptl.entry_id 1RQQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 580.298 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER' _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 1RQQ _cell.length_a 87.216 _cell.length_b 96.443 _cell.length_c 121.993 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RQQ _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 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 ? 5 I N N ? 5 J 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 covale ? covale1 A C ILE 180 A ILE 1157 1_555 A N PTR 181 A PTR 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C PTR 181 A PTR 1158 1_555 A N GLU 182 A GLU 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C ASP 184 A ASP 1161 1_555 A N PTR 185 A PTR 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C PTR 185 A PTR 1162 1_555 A N PTR 186 A PTR 1163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A C PTR 186 A PTR 1163 1_555 A N ARG 187 A ARG 1164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 B C ILE 180 B ILE 1157 1_555 B N PTR 181 B PTR 1158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 B C PTR 181 B PTR 1158 1_555 B N GLU 182 B GLU 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 B C ASP 184 B ASP 1161 1_555 B N PTR 185 B PTR 1162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 B C PTR 185 B PTR 1162 1_555 B N PTR 186 B PTR 1163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 B C PTR 186 B PTR 1163 1_555 B N ARG 187 B ARG 1164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 E CZ PHE 10 E PHE 108 1_555 I NS 112 . E 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale12 F CZ PHE 10 F PHE 108 1_555 J NS 112 . F 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? metalc ? metalc1 K O HOH . A HOH 63 1_555 G MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc2 G MN MN . A MN 201 1_555 A OD1 ASN 160 A ASN 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc3 G MN MN . A MN 201 1_555 A OD2 ASP 173 A ASP 1150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 G MN MN . A MN 201 1_555 I O2S 112 . E 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc5 G MN MN . A MN 201 1_555 I O2G 112 . E 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc6 G MN MN . A MN 201 1_555 I O2B 112 . E 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc7 H MN MN . B MN 202 1_555 B OD1 ASN 160 B ASN 1137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc8 H MN MN . B MN 202 1_555 B OD2 ASP 173 B ASP 1150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc9 H MN MN . B MN 202 1_555 P O HOH . F HOH 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc10 H MN MN . B MN 202 1_555 J O2G 112 . F 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc11 H MN MN . B MN 202 1_555 J O2S 112 . F 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc12 H MN MN . B MN 202 1_555 J O2B 112 . F 112 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? # _chem_comp.formula 'C12 H19 N6 O13 P3 S' _chem_comp.formula_weight 580.298 _chem_comp.id 112 _chem_comp.mon_nstd_flag . _chem_comp.name 'THIOPHOSPHORIC ACID O-((ADENOSYL-PHOSPHO)PHOSPHO)-S-ACETAMIDYL-DIESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 NS C2S 112 sing 1 n n NS HNS1 112 sing 2 n n NS HNS2 112 sing 3 n n C2S O2S 112 doub 4 n n C2S C1S 112 sing 5 n n C1S S1G 112 sing 6 n n C1S H1S1 112 sing 7 n n C1S H1S2 112 sing 8 n n PG S1G 112 sing 9 n n PG O2G 112 sing 10 n n PG O3G 112 doub 11 n n PG O3B 112 sing 12 n n O2G HOG2 112 sing 13 n n PB O1B 112 doub 14 n n PB O2B 112 sing 15 n n PB O3B 112 sing 16 n n PB O3A 112 sing 17 n n O2B HOB2 112 sing 18 n n PA O1A 112 doub 19 n n PA O2A 112 sing 20 n n PA O3A 112 sing 21 n n PA O5' 112 sing 22 n n O2A HOA2 112 sing 23 n n O5' C5' 112 sing 24 n n C5' C4' 112 sing 25 n n C5' "H5'1" 112 sing 26 n n C5' "H5'2" 112 sing 27 n n C4' O4' 112 sing 28 n n C4' C3' 112 sing 29 n n C4' H4' 112 sing 30 n n O4' C1' 112 sing 31 n n C3' O3' 112 sing 32 n n C3' C2' 112 sing 33 n n C3' H3' 112 sing 34 n n O3' HO3' 112 sing 35 n n C2' O2' 112 sing 36 n n C2' C1' 112 sing 37 n n C2' H2' 112 sing 38 n n O2' HO2' 112 sing 39 n n C1' N9 112 sing 40 n n C1' H1' 112 sing 41 n n N9 C8 112 sing 42 n y N9 C4 112 sing 43 n y C8 N7 112 doub 44 n y C8 H8 112 sing 45 n n N7 C5 112 sing 46 n y C5 C6 112 sing 47 n y C5 C4 112 doub 48 n y C6 N6 112 sing 49 n n C6 N1 112 doub 50 n y N6 HN61 112 sing 51 n n N6 HN62 112 sing 52 n n N1 C2 112 sing 53 n y C2 N3 112 doub 54 n y C2 H2 112 sing 55 n n N3 C4 112 sing 56 n y # _atom_sites.entry_id 1RQQ _atom_sites.fract_transf_matrix[1][1] 0.011466 _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] 0.010369 _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] 0.008197 _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 4 MN A 1 201 201 MN MN . H 4 MN B 1 202 202 MN MN . I 5 112 E 1 117 101 112 112 . J 5 112 F 1 117 101 112 112 . K 6 HOH A 1 1 1 HOH HOH . K 6 HOH A 2 2 2 HOH HOH . K 6 HOH A 3 3 3 HOH HOH . K 6 HOH A 4 5 5 HOH HOH . K 6 HOH A 5 8 8 HOH HOH . K 6 HOH A 6 14 14 HOH HOH . K 6 HOH A 7 15 15 HOH HOH . K 6 HOH A 8 17 17 HOH HOH . K 6 HOH A 9 18 18 HOH HOH . K 6 HOH A 10 21 21 HOH HOH . K 6 HOH A 11 22 22 HOH HOH . K 6 HOH A 12 25 25 HOH HOH . K 6 HOH A 13 27 27 HOH HOH . K 6 HOH A 14 28 28 HOH HOH . K 6 HOH A 15 30 30 HOH HOH . K 6 HOH A 16 33 33 HOH HOH . K 6 HOH A 17 39 39 HOH HOH . K 6 HOH A 18 41 41 HOH HOH . K 6 HOH A 19 42 42 HOH HOH . K 6 HOH A 20 43 43 HOH HOH . K 6 HOH A 21 44 44 HOH HOH . K 6 HOH A 22 46 46 HOH HOH . K 6 HOH A 23 47 47 HOH HOH . K 6 HOH A 24 48 48 HOH HOH . K 6 HOH A 25 51 51 HOH HOH . K 6 HOH A 26 52 52 HOH HOH . K 6 HOH A 27 53 53 HOH HOH . K 6 HOH A 28 54 54 HOH HOH . K 6 HOH A 29 57 57 HOH HOH . K 6 HOH A 30 59 59 HOH HOH . K 6 HOH A 31 60 60 HOH HOH . K 6 HOH A 32 63 63 HOH HOH . K 6 HOH A 33 69 69 HOH HOH . K 6 HOH A 34 71 71 HOH HOH . K 6 HOH A 35 73 73 HOH HOH . K 6 HOH A 36 75 75 HOH HOH . K 6 HOH A 37 76 76 HOH HOH . L 6 HOH B 1 4 4 HOH HOH . L 6 HOH B 2 6 6 HOH HOH . L 6 HOH B 3 7 7 HOH HOH . L 6 HOH B 4 9 9 HOH HOH . L 6 HOH B 5 10 10 HOH HOH . L 6 HOH B 6 12 12 HOH HOH . L 6 HOH B 7 13 13 HOH HOH . L 6 HOH B 8 16 16 HOH HOH . L 6 HOH B 9 19 19 HOH HOH . L 6 HOH B 10 20 20 HOH HOH . L 6 HOH B 11 24 24 HOH HOH . L 6 HOH B 12 31 31 HOH HOH . L 6 HOH B 13 32 32 HOH HOH . L 6 HOH B 14 34 34 HOH HOH . L 6 HOH B 15 35 35 HOH HOH . L 6 HOH B 16 38 38 HOH HOH . L 6 HOH B 17 45 45 HOH HOH . L 6 HOH B 18 49 49 HOH HOH . L 6 HOH B 19 50 50 HOH HOH . L 6 HOH B 20 65 65 HOH HOH . L 6 HOH B 21 67 67 HOH HOH . L 6 HOH B 22 68 68 HOH HOH . L 6 HOH B 23 70 70 HOH HOH . L 6 HOH B 24 74 74 HOH HOH . L 6 HOH B 25 77 77 HOH HOH . M 6 HOH C 1 23 23 HOH HOH . M 6 HOH C 2 36 36 HOH HOH . M 6 HOH C 3 40 40 HOH HOH . M 6 HOH C 4 79 79 HOH HOH . N 6 HOH D 1 26 26 HOH HOH . N 6 HOH D 2 37 37 HOH HOH . N 6 HOH D 3 55 55 HOH HOH . N 6 HOH D 4 56 56 HOH HOH . N 6 HOH D 5 58 58 HOH HOH . N 6 HOH D 6 72 72 HOH HOH . N 6 HOH D 7 78 78 HOH HOH . O 6 HOH E 1 61 61 HOH HOH . O 6 HOH E 2 62 62 HOH HOH . O 6 HOH E 3 64 64 HOH HOH . P 6 HOH F 1 11 11 HOH HOH . P 6 HOH F 2 29 29 HOH HOH . P 6 HOH F 3 66 66 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 N NS 112 . . . J 5 -8.716 32.045 -7.833 1 48.67 ? NS 112 117 F 1 HETATM 2 C C2S 112 . . . J 5 -8.37 33.277 -7.477 1 50.9 ? C2S 112 117 F 1 HETATM 3 O O2S 112 . . . J 5 -7.166 33.46 -7.363 1 48.67 ? O2S 112 117 F 1 HETATM 4 C C1S 112 . . . J 5 -9.353 34.429 -7.207 1 54.22 ? C1S 112 117 F 1 HETATM 5 P PG 112 . . . J 5 -8.546 37.302 -8.172 1 52.47 ? PG 112 117 F 1 HETATM 6 S S1G 112 . . . J 5 -9.657 35.645 -8.573 1 62.22 ? S1G 112 117 F 1 HETATM 7 O O2G 112 . . . J 5 -7.075 36.98 -8.189 1 53.78 ? O2G 112 117 F 1 HETATM 8 O O3G 112 . . . J 5 -8.879 38.388 -9.113 1 53.84 ? O3G 112 117 F 1 HETATM 9 P PB 112 . . . J 5 -8.726 37.289 -5.344 1 42.25 ? PB 112 117 F 1 HETATM 10 O O1B 112 . . . J 5 -9.968 37.018 -4.637 1 47.48 ? O1B 112 117 F 1 HETATM 11 O O2B 112 . . . J 5 -7.654 36.299 -5.198 1 46.63 ? O2B 112 117 F 1 HETATM 12 O O3B 112 . . . J 5 -8.868 37.826 -6.767 1 48.56 ? O3B 112 117 F 1 HETATM 13 P PA 112 . . . J 5 -7.199 39.21 -3.888 1 48.41 ? PA 112 117 F 1 HETATM 14 O O1A 112 . . . J 5 -7.785 39.021 -2.555 1 48.83 ? O1A 112 117 F 1 HETATM 15 O O2A 112 . . . J 5 -5.832 38.676 -4.124 1 51.74 ? O2A 112 117 F 1 HETATM 16 O O3A 112 . . . J 5 -8.204 38.659 -4.903 1 48.33 ? O3A 112 117 F 1 HETATM 17 O O5' 112 . . . J 5 -7.122 40.802 -4.247 1 47.2 ? O5' 112 117 F 1 HETATM 18 C C5' 112 . . . J 5 -8.034 41.764 -4.89 1 45.4 ? C5' 112 117 F 1 HETATM 19 C C4' 112 . . . J 5 -7.18 42.577 -5.831 1 44.33 ? C4' 112 117 F 1 HETATM 20 O O4' 112 . . . J 5 -6.086 43.13 -5.077 1 43.73 ? O4' 112 117 F 1 HETATM 21 C C3' 112 . . . J 5 -6.52 41.743 -6.918 1 47.04 ? C3' 112 117 F 1 HETATM 22 O O3' 112 . . . J 5 -7.345 41.768 -8.074 1 50.46 ? O3' 112 117 F 1 HETATM 23 C C2' 112 . . . J 5 -5.186 42.433 -7.195 1 44.16 ? C2' 112 117 F 1 HETATM 24 O O2' 112 . . . J 5 -5.231 43.273 -8.328 1 50.71 ? O2' 112 117 F 1 HETATM 25 C C1' 112 . . . J 5 -4.952 43.243 -5.912 1 42.89 ? C1' 112 117 F 1 HETATM 26 N N9 112 . . . J 5 -3.758 42.923 -5.133 1 40.61 ? N9 112 117 F 1 HETATM 27 C C8 112 . . . J 5 -3.537 41.858 -4.295 1 39.73 ? C8 112 117 F 1 HETATM 28 N N7 112 . . . J 5 -2.34 41.855 -3.753 1 38.38 ? N7 112 117 F 1 HETATM 29 C C5 112 . . . J 5 -1.732 42.989 -4.269 1 37.28 ? C5 112 117 F 1 HETATM 30 C C6 112 . . . J 5 -0.444 43.542 -4.104 1 36.49 ? C6 112 117 F 1 HETATM 31 N N6 112 . . . J 5 0.511 42.999 -3.344 1 34.44 ? N6 112 117 F 1 HETATM 32 N N1 112 . . . J 5 -0.162 44.686 -4.763 1 37.3 ? N1 112 117 F 1 HETATM 33 C C2 112 . . . J 5 -1.112 45.234 -5.534 1 37.2 ? C2 112 117 F 1 HETATM 34 N N3 112 . . . J 5 -2.353 44.811 -5.771 1 39.41 ? N3 112 117 F 1 HETATM 35 C C4 112 . . . J 5 -2.602 43.666 -5.108 1 39.06 ? C4 112 117 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #