data_8ROK # _model_server_result.job_id RYWzLyz2AifhZ-T0ChLbGA _model_server_result.datetime_utc '2024-11-05 23:41:22' _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 8rok # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2001}' # _entry.id 8ROK # _exptl.entry_id 8ROK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _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 8ROK _cell.length_a 118.244 _cell.length_b 154.459 _cell.length_c 136.541 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ROK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I 1 1 C,D,G,H,J,K 2 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 ? 3 E N N ? 3 H 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 39 A SER 39 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc2 E O2G AGS . A AGS 2001 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 E O2B AGS . A AGS 2001 1_555 F MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc4 F MG MG . A MG 2002 1_555 I O HOH . A HOH 2117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc5 F MG MG . A MG 2002 1_555 I O HOH . A HOH 2128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc6 F MG MG . A MG 2002 1_555 I O HOH . A HOH 2136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc7 C OG SER 39 C SER 39 1_555 G MG MG . C MG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc8 G MG MG . C MG 2000 1_555 H O2G AGS . C AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc9 G MG MG . C MG 2000 1_555 H O2B AGS . C AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc10 G MG MG . C MG 2000 1_555 J O HOH . C HOH 2110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc11 G MG MG . C MG 2000 1_555 J O HOH . C HOH 2118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc12 G MG MG . C MG 2000 1_555 J O HOH . C HOH 2134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 8ROK _atom_sites.fract_transf_matrix[1][1] 0.008457 _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] 0.006474 _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] 0.007324 _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 E 3 AGS A 1 2001 2001 AGS AGS . F 4 MG A 1 2002 2000 MG MG . G 4 MG C 1 2000 2000 MG MG . H 3 AGS C 1 2001 2001 AGS AGS . I 5 HOH A 1 2101 77 HOH HOH . I 5 HOH A 2 2102 92 HOH HOH . I 5 HOH A 3 2103 101 HOH HOH . I 5 HOH A 4 2104 119 HOH HOH . I 5 HOH A 5 2105 120 HOH HOH . I 5 HOH A 6 2106 100 HOH HOH . I 5 HOH A 7 2107 91 HOH HOH . I 5 HOH A 8 2108 73 HOH HOH . I 5 HOH A 9 2109 82 HOH HOH . I 5 HOH A 10 2110 78 HOH HOH . I 5 HOH A 11 2111 118 HOH HOH . I 5 HOH A 12 2112 123 HOH HOH . I 5 HOH A 13 2113 12 HOH HOH . I 5 HOH A 14 2114 88 HOH HOH . I 5 HOH A 15 2115 10 HOH HOH . I 5 HOH A 16 2116 116 HOH HOH . I 5 HOH A 17 2117 4 HOH HOH . I 5 HOH A 18 2118 7 HOH HOH . I 5 HOH A 19 2119 86 HOH HOH . I 5 HOH A 20 2120 94 HOH HOH . I 5 HOH A 21 2121 57 HOH HOH . I 5 HOH A 22 2122 48 HOH HOH . I 5 HOH A 23 2123 19 HOH HOH . I 5 HOH A 24 2124 108 HOH HOH . I 5 HOH A 25 2125 51 HOH HOH . I 5 HOH A 26 2126 74 HOH HOH . I 5 HOH A 27 2127 29 HOH HOH . I 5 HOH A 28 2128 6 HOH HOH . I 5 HOH A 29 2129 70 HOH HOH . I 5 HOH A 30 2130 90 HOH HOH . I 5 HOH A 31 2131 97 HOH HOH . I 5 HOH A 32 2132 115 HOH HOH . I 5 HOH A 33 2133 93 HOH HOH . I 5 HOH A 34 2134 21 HOH HOH . I 5 HOH A 35 2135 54 HOH HOH . I 5 HOH A 36 2136 5 HOH HOH . I 5 HOH A 37 2137 85 HOH HOH . I 5 HOH A 38 2138 31 HOH HOH . I 5 HOH A 39 2139 35 HOH HOH . I 5 HOH A 40 2140 96 HOH HOH . I 5 HOH A 41 2141 87 HOH HOH . I 5 HOH A 42 2142 103 HOH HOH . I 5 HOH A 43 2143 89 HOH HOH . I 5 HOH A 44 2144 71 HOH HOH . I 5 HOH A 45 2145 127 HOH HOH . I 5 HOH A 46 2146 66 HOH HOH . I 5 HOH A 47 2147 64 HOH HOH . J 5 HOH C 1 2101 37 HOH HOH . J 5 HOH C 2 2102 41 HOH HOH . J 5 HOH C 3 2103 84 HOH HOH . J 5 HOH C 4 2104 17 HOH HOH . J 5 HOH C 5 2105 104 HOH HOH . J 5 HOH C 6 2106 114 HOH HOH . J 5 HOH C 7 2107 112 HOH HOH . J 5 HOH C 8 2108 109 HOH HOH . J 5 HOH C 9 2109 20 HOH HOH . J 5 HOH C 10 2110 1 HOH HOH . J 5 HOH C 11 2111 111 HOH HOH . J 5 HOH C 12 2112 75 HOH HOH . J 5 HOH C 13 2113 124 HOH HOH . J 5 HOH C 14 2114 15 HOH HOH . J 5 HOH C 15 2115 8 HOH HOH . J 5 HOH C 16 2116 106 HOH HOH . J 5 HOH C 17 2117 9 HOH HOH . J 5 HOH C 18 2118 3 HOH HOH . J 5 HOH C 19 2119 113 HOH HOH . J 5 HOH C 20 2120 105 HOH HOH . J 5 HOH C 21 2121 11 HOH HOH . J 5 HOH C 22 2122 34 HOH HOH . J 5 HOH C 23 2123 110 HOH HOH . J 5 HOH C 24 2124 22 HOH HOH . J 5 HOH C 25 2125 44 HOH HOH . J 5 HOH C 26 2126 107 HOH HOH . J 5 HOH C 27 2127 36 HOH HOH . J 5 HOH C 28 2128 13 HOH HOH . J 5 HOH C 29 2129 53 HOH HOH . J 5 HOH C 30 2130 30 HOH HOH . J 5 HOH C 31 2131 125 HOH HOH . J 5 HOH C 32 2132 81 HOH HOH . J 5 HOH C 33 2133 40 HOH HOH . J 5 HOH C 34 2134 2 HOH HOH . J 5 HOH C 35 2135 42 HOH HOH . J 5 HOH C 36 2136 122 HOH HOH . J 5 HOH C 37 2137 121 HOH HOH . J 5 HOH C 38 2138 18 HOH HOH . J 5 HOH C 39 2139 126 HOH HOH . K 5 HOH D 1 201 52 HOH HOH . K 5 HOH D 2 202 26 HOH HOH . K 5 HOH D 3 203 55 HOH HOH . K 5 HOH D 4 204 128 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 . . . E 3 -27.028 36.197 26.612 1 43.72 ? PG AGS 2001 A 1 HETATM 2 S S1G AGS . . . E 3 -25.541 35.422 27.549 1 43.59 ? S1G AGS 2001 A 1 HETATM 3 O O2G AGS . . . E 3 -28.435 35.368 26.788 1 37.54 ? O2G AGS 2001 A 1 HETATM 4 O O3G AGS . . . E 3 -27.182 37.772 26.969 1 52.67 ? O3G AGS 2001 A 1 HETATM 5 P PB AGS . . . E 3 -26.965 34.924 23.958 1 45.48 ? PB AGS 2001 A 1 HETATM 6 O O1B AGS . . . E 3 -25.638 34.397 23.452 1 44.96 -1 O1B AGS 2001 A 1 HETATM 7 O O2B AGS . . . E 3 -27.831 33.837 24.566 1 42.18 ? O2B AGS 2001 A 1 HETATM 8 O O3B AGS . . . E 3 -26.59 36.119 25.018 1 50.94 ? O3B AGS 2001 A 1 HETATM 9 P PA AGS . . . E 3 -29.035 35.088 21.916 1 45.29 ? PA AGS 2001 A 1 HETATM 10 O O1A AGS . . . E 3 -28.553 33.787 21.262 1 49.07 -1 O1A AGS 2001 A 1 HETATM 11 O O2A AGS . . . E 3 -30.321 34.831 22.663 1 44.39 ? O2A AGS 2001 A 1 HETATM 12 O O3A AGS . . . E 3 -27.777 35.671 22.776 1 46.8 ? O3A AGS 2001 A 1 HETATM 13 O O5' AGS . . . E 3 -29.335 36.319 20.795 1 39.41 ? O5' AGS 2001 A 1 HETATM 14 C C5' AGS . . . E 3 -28.205 36.753 20.015 1 42.12 ? C5' AGS 2001 A 1 HETATM 15 C C4' AGS . . . E 3 -28.688 37.905 19.141 1 51.98 ? C4' AGS 2001 A 1 HETATM 16 O O4' AGS . . . E 3 -29.611 37.466 18.323 1 49.89 ? O4' AGS 2001 A 1 HETATM 17 C C3' AGS . . . E 3 -29.414 38.973 20.09 1 54 ? C3' AGS 2001 A 1 HETATM 18 O O3' AGS . . . E 3 -28.843 40.155 19.939 1 46.72 ? O3' AGS 2001 A 1 HETATM 19 C C2' AGS . . . E 3 -30.88 38.969 19.604 1 56.53 ? C2' AGS 2001 A 1 HETATM 20 O O2' AGS . . . E 3 -31.488 40.295 19.804 1 48.79 ? O2' AGS 2001 A 1 HETATM 21 C C1' AGS . . . E 3 -30.771 38.615 18.305 1 53.23 ? C1' AGS 2001 A 1 HETATM 22 N N9 AGS . . . E 3 -31.958 38.092 17.722 1 46.88 ? N9 AGS 2001 A 1 HETATM 23 C C8 AGS . . . E 3 -32.965 37.497 18.335 1 45.55 ? C8 AGS 2001 A 1 HETATM 24 N N7 AGS . . . E 3 -33.913 37.174 17.456 1 50.3 ? N7 AGS 2001 A 1 HETATM 25 C C5 AGS . . . E 3 -33.497 37.54 16.223 1 49.97 ? C5 AGS 2001 A 1 HETATM 26 C C6 AGS . . . E 3 -34.019 37.466 14.911 1 55.04 ? C6 AGS 2001 A 1 HETATM 27 N N6 AGS . . . E 3 -35.316 36.861 14.673 1 48.02 ? N6 AGS 2001 A 1 HETATM 28 N N1 AGS . . . E 3 -33.319 37.959 13.898 1 52.48 ? N1 AGS 2001 A 1 HETATM 29 C C2 AGS . . . E 3 -32.131 38.529 14.11 1 50.84 ? C2 AGS 2001 A 1 HETATM 30 N N3 AGS . . . E 3 -31.6 38.618 15.315 1 52.22 ? N3 AGS 2001 A 1 HETATM 31 C C4 AGS . . . E 3 -32.258 38.139 16.398 1 51.52 ? C4 AGS 2001 A 1 # _model_server_stats.io_time_ms 168 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #