data_8ROL # _model_server_result.job_id gEa4fJsbALyNq4SMMFZo8w _model_server_result.datetime_utc '2024-11-05 19:51:10' _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 8rol # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 8ROL # _exptl.entry_id 8ROL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 8ROL _cell.length_a 201.067 _cell.length_b 201.067 _cell.length_c 92.376 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ROL _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall 'P 64 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 C MG MG . A MG 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 C MG MG . A MG 2000 1_555 D O2G AGS . A AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc3 C MG MG . A MG 2000 1_555 D O2B AGS . A AGS 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? # _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 8ROL _atom_sites.fract_transf_matrix[1][1] 0.004973 _atom_sites.fract_transf_matrix[1][2] 0.002871 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005743 _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] 0.010825 _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 C 3 MG A 1 2000 2000 MG MG . D 4 AGS A 1 2001 2001 AGS AGS . # 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 . . . D 4 82.124 51.223 -5.225 1 90.24 ? PG AGS 2001 A 1 HETATM 2 S S1G AGS . . . D 4 83.532 52.13 -6.194 1 105.6 ? S1G AGS 2001 A 1 HETATM 3 O O2G AGS . . . D 4 80.651 51.528 -5.944 1 91.94 ? O2G AGS 2001 A 1 HETATM 4 O O3G AGS . . . D 4 82.483 49.638 -5.14 1 115.18 ? O3G AGS 2001 A 1 HETATM 5 P PB AGS . . . D 4 81.206 52.981 -3.238 1 98.33 ? PB AGS 2001 A 1 HETATM 6 O O1B AGS . . . D 4 82.078 54.192 -3.466 1 87.16 -1 O1B AGS 2001 A 1 HETATM 7 O O2B AGS . . . D 4 80.006 52.979 -4.114 1 87.49 ? O2B AGS 2001 A 1 HETATM 8 O O3B AGS . . . D 4 82.099 51.7 -3.671 1 85.96 ? O3B AGS 2001 A 1 HETATM 9 P PA AGS . . . D 4 79.225 52.603 -1.284 1 78.91 ? PA AGS 2001 A 1 HETATM 10 O O1A AGS . . . D 4 78.664 54.01 -1.252 1 94.09 -1 O1A AGS 2001 A 1 HETATM 11 O O2A AGS . . . D 4 78.488 51.711 -2.262 1 68.66 ? O2A AGS 2001 A 1 HETATM 12 O O3A AGS . . . D 4 80.772 52.866 -1.693 1 80.14 ? O3A AGS 2001 A 1 HETATM 13 O O5' AGS . . . D 4 79.172 52.018 0.268 1 85.05 ? O5' AGS 2001 A 1 HETATM 14 C C5' AGS . . . D 4 80.394 52.259 0.986 1 88.62 ? C5' AGS 2001 A 1 HETATM 15 C C4' AGS . . . D 4 80.417 51.476 2.289 1 96.63 ? C4' AGS 2001 A 1 HETATM 16 O O4' AGS . . . D 4 79.266 51.649 2.885 1 89.62 ? O4' AGS 2001 A 1 HETATM 17 C C3' AGS . . . D 4 80.573 49.891 2.056 1 107.56 ? C3' AGS 2001 A 1 HETATM 18 O O3' AGS . . . D 4 81.637 49.374 2.703 1 100.66 ? O3' AGS 2001 A 1 HETATM 19 C C2' AGS . . . D 4 79.256 49.309 2.62 1 106.68 ? C2' AGS 2001 A 1 HETATM 20 O O2' AGS . . . D 4 79.468 47.94 3.131 1 97.41 ? O2' AGS 2001 A 1 HETATM 21 C C1' AGS . . . D 4 78.959 50.194 3.586 1 101.12 ? C1' AGS 2001 A 1 HETATM 22 N N9 AGS . . . D 4 77.601 50.177 3.983 1 96.3 ? N9 AGS 2001 A 1 HETATM 23 C C8 AGS . . . D 4 76.56 49.883 3.22 1 95.28 ? C8 AGS 2001 A 1 HETATM 24 N N7 AGS . . . D 4 75.443 49.981 3.939 1 95.26 ? N7 AGS 2001 A 1 HETATM 25 C C5 AGS . . . D 4 75.763 50.351 5.188 1 94.25 ? C5 AGS 2001 A 1 HETATM 26 C C6 AGS . . . D 4 75.054 50.61 6.363 1 97.45 ? C6 AGS 2001 A 1 HETATM 27 N N6 AGS . . . D 4 73.609 50.484 6.347 1 94.56 ? N6 AGS 2001 A 1 HETATM 28 N N1 AGS . . . D 4 75.697 50.961 7.468 1 98.68 ? N1 AGS 2001 A 1 HETATM 29 C C2 AGS . . . D 4 77.016 51.074 7.462 1 96.53 ? C2 AGS 2001 A 1 HETATM 30 N N3 AGS . . . D 4 77.71 50.839 6.359 1 99.49 ? N3 AGS 2001 A 1 HETATM 31 C C4 AGS . . . D 4 77.13 50.48 5.212 1 97.47 ? C4 AGS 2001 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #