data_8ROB # _model_server_result.job_id 73aMtYxRTkZdoNQ1IQYNxg _model_server_result.datetime_utc '2024-11-22 22:20:15' _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 8rob # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1302}' # _entry.id 8ROB # _exptl.entry_id 8ROB _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 90 _cell.entry_id 8ROB _cell.length_a 68.923 _cell.length_b 68.923 _cell.length_c 215.327 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ROB _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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,E,F _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 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc2 A OE1 GLN 137 A GLN 137 1_555 C MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc3 C MG MG . A MG 1301 1_555 D O2B AGS . A AGS 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc4 C MG MG . A MG 1301 1_555 D O2G AGS . A AGS 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc5 C MG MG . A MG 1301 1_555 E O HOH . A HOH 1408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? # _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 8ROB _atom_sites.fract_transf_matrix[1][1] 0.014509 _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] 0.014509 _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] 0.004644 _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 1301 1500 MG MG . D 4 AGS A 1 1302 1600 AGS AGS . E 5 HOH A 1 1401 17 HOH HOH . E 5 HOH A 2 1402 8 HOH HOH . E 5 HOH A 3 1403 23 HOH HOH . E 5 HOH A 4 1404 15 HOH HOH . E 5 HOH A 5 1405 27 HOH HOH . E 5 HOH A 6 1406 1 HOH HOH . E 5 HOH A 7 1407 4 HOH HOH . E 5 HOH A 8 1408 31 HOH HOH . E 5 HOH A 9 1409 5 HOH HOH . E 5 HOH A 10 1410 3 HOH HOH . E 5 HOH A 11 1411 11 HOH HOH . E 5 HOH A 12 1412 2 HOH HOH . E 5 HOH A 13 1413 19 HOH HOH . E 5 HOH A 14 1414 22 HOH HOH . E 5 HOH A 15 1415 7 HOH HOH . E 5 HOH A 16 1416 18 HOH HOH . E 5 HOH A 17 1417 24 HOH HOH . E 5 HOH A 18 1418 10 HOH HOH . E 5 HOH A 19 1419 25 HOH HOH . E 5 HOH A 20 1420 29 HOH HOH . E 5 HOH A 21 1421 26 HOH HOH . E 5 HOH A 22 1422 13 HOH HOH . E 5 HOH A 23 1423 9 HOH HOH . E 5 HOH A 24 1424 20 HOH HOH . E 5 HOH A 25 1425 6 HOH HOH . E 5 HOH A 26 1426 30 HOH HOH . E 5 HOH A 27 1427 21 HOH HOH . F 5 HOH B 1 701 16 HOH HOH . F 5 HOH B 2 702 14 HOH HOH . F 5 HOH B 3 703 28 HOH HOH . F 5 HOH B 4 704 12 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 . . . D 4 7.039 5.316 -12.201 1 58.35 ? PG AGS 1302 A 1 HETATM 2 S S1G AGS . . . D 4 5.332 4.687 -11.579 1 59.89 ? S1G AGS 1302 A 1 HETATM 3 O O2G AGS . . . D 4 7.302 6.875 -11.756 1 60.26 ? O2G AGS 1302 A 1 HETATM 4 O O3G AGS . . . D 4 8.294 4.369 -11.778 1 67.26 ? O3G AGS 1302 A 1 HETATM 5 P PB AGS . . . D 4 6.273 6.222 -14.856 1 64.29 ? PB AGS 1302 A 1 HETATM 6 O O1B AGS . . . D 4 4.915 5.667 -15.155 1 54 ? O1B AGS 1302 A 1 HETATM 7 O O2B AGS . . . D 4 6.191 7.635 -14.398 1 59.58 ? O2B AGS 1302 A 1 HETATM 8 O O3B AGS . . . D 4 7.071 5.244 -13.834 1 67.13 ? O3B AGS 1302 A 1 HETATM 9 P PA AGS . . . D 4 7.707 7.434 -17.085 1 59.69 ? PA AGS 1302 A 1 HETATM 10 O O1A AGS . . . D 4 6.486 8.24 -17.53 1 56.52 ? O1A AGS 1302 A 1 HETATM 11 O O2A AGS . . . D 4 8.708 8.298 -16.346 1 56.64 ? O2A AGS 1302 A 1 HETATM 12 O O3A AGS . . . D 4 7.206 6.169 -16.176 1 65.93 ? O3A AGS 1302 A 1 HETATM 13 O O5' AGS . . . D 4 8.481 6.674 -18.344 1 68.87 ? O5' AGS 1302 A 1 HETATM 14 C C5' AGS . . . D 4 7.768 5.6 -18.943 1 70.75 ? C5' AGS 1302 A 1 HETATM 15 C C4' AGS . . . D 4 8.666 5.245 -20.09 1 76.35 ? C4' AGS 1302 A 1 HETATM 16 O O4' AGS . . . D 4 8.736 6.273 -20.881 1 75.17 ? O4' AGS 1302 A 1 HETATM 17 C C3' AGS . . . D 4 10.172 5.12 -19.569 1 76.01 ? C3' AGS 1302 A 1 HETATM 18 O O3' AGS . . . D 4 10.434 3.849 -19.239 1 66.3 ? O3' AGS 1302 A 1 HETATM 19 C C2' AGS . . . D 4 11.009 5.603 -20.79 1 80.05 ? C2' AGS 1302 A 1 HETATM 20 O O2' AGS . . . D 4 11.973 4.569 -21.24 1 78.08 ? O2' AGS 1302 A 1 HETATM 21 C C1' AGS . . . D 4 10.081 5.862 -21.74 1 78.97 ? C1' AGS 1302 A 1 HETATM 22 N N9 AGS . . . D 4 10.463 6.898 -22.639 1 77.97 ? N9 AGS 1302 A 1 HETATM 23 C C8 AGS . . . D 4 11.022 8.073 -22.347 1 83.51 ? C8 AGS 1302 A 1 HETATM 24 N N7 AGS . . . D 4 11.227 8.776 -23.455 1 74.72 ? N7 AGS 1302 A 1 HETATM 25 C C5 AGS . . . D 4 10.796 8.032 -24.5 1 73.53 ? C5 AGS 1302 A 1 HETATM 26 C C6 AGS . . . D 4 10.75 8.191 -25.907 1 67.01 ? C6 AGS 1302 A 1 HETATM 27 N N6 AGS . . . D 4 11.249 9.398 -26.515 1 54.54 ? N6 AGS 1302 A 1 HETATM 28 N N1 AGS . . . D 4 10.249 7.232 -26.664 1 61.12 ? N1 AGS 1302 A 1 HETATM 29 C C2 AGS . . . D 4 9.791 6.107 -26.1 1 67.11 ? C2 AGS 1302 A 1 HETATM 30 N N3 AGS . . . D 4 9.826 5.92 -24.781 1 68.04 ? N3 AGS 1302 A 1 HETATM 31 C C4 AGS . . . D 4 10.315 6.85 -23.966 1 65.13 ? C4 AGS 1302 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #