data_3EUJ # _model_server_result.job_id GfCdaAw6Y21ei6CtH9gSzg _model_server_result.datetime_utc '2025-04-22 16:58:16' _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 3euj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2001}' # _entry.id 3EUJ # _exptl.entry_id 3EUJ _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 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 3EUJ _cell.length_a 58.522 _cell.length_b 180.203 _cell.length_c 138.496 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EUJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 17 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 58.522 0 69.248 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 43 A SER 72 1_555 D MG MG . A MG 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc2 C O2G AGS . A AGS 2001 1_555 D MG MG . A MG 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc3 C O2A AGS . A AGS 2001 1_555 D MG MG . A MG 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc4 C O1B AGS . A AGS 2001 1_555 D MG MG . A MG 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? # _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 3EUJ _atom_sites.fract_transf_matrix[1][1] 0.017088 _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] 0.005549 _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] 0.00722 _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 AGS A 1 2001 2001 AGS ATG . D 4 MG A 1 2011 2011 MG MG . E 5 HOH A 1 2012 1 HOH HOH . E 5 HOH A 2 2013 2 HOH HOH . E 5 HOH A 3 2014 4 HOH HOH . E 5 HOH A 4 2015 5 HOH HOH . E 5 HOH A 5 2016 6 HOH HOH . E 5 HOH A 6 2017 7 HOH HOH . E 5 HOH A 7 2018 11 HOH HOH . E 5 HOH A 8 2019 12 HOH HOH . E 5 HOH A 9 2020 13 HOH HOH . E 5 HOH A 10 2021 16 HOH HOH . E 5 HOH A 11 2022 17 HOH HOH . E 5 HOH A 12 2023 18 HOH HOH . E 5 HOH A 13 2024 19 HOH HOH . E 5 HOH A 14 2025 20 HOH HOH . E 5 HOH A 15 2026 21 HOH HOH . E 5 HOH A 16 2027 22 HOH HOH . E 5 HOH A 17 2028 23 HOH HOH . E 5 HOH A 18 2029 24 HOH HOH . E 5 HOH A 19 2030 25 HOH HOH . E 5 HOH A 20 2031 27 HOH HOH . E 5 HOH A 21 2032 28 HOH HOH . E 5 HOH A 22 2033 29 HOH HOH . E 5 HOH A 23 2034 30 HOH HOH . F 5 HOH B 1 3 3 HOH HOH . F 5 HOH B 2 8 8 HOH HOH . F 5 HOH B 3 9 9 HOH HOH . F 5 HOH B 4 10 10 HOH HOH . F 5 HOH B 5 14 14 HOH HOH . F 5 HOH B 6 15 15 HOH HOH . F 5 HOH B 7 26 26 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 . . . C 3 20.482 78.267 31.192 1 32.38 ? PG AGS 2001 A 1 HETATM 2 S S1G AGS . . . C 3 21.355 79.848 31.317 1 39.97 ? S1G AGS 2001 A 1 HETATM 3 O O2G AGS . . . C 3 21.465 77.292 30.564 1 33.57 ? O2G AGS 2001 A 1 HETATM 4 O O3G AGS . . . C 3 19.836 77.813 32.436 1 28.9 ? O3G AGS 2001 A 1 HETATM 5 P PB AGS . . . C 3 18.966 78.372 28.673 1 27.6 ? PB AGS 2001 A 1 HETATM 6 O O1B AGS . . . C 3 20.124 77.701 28.032 1 27.11 ? O1B AGS 2001 A 1 HETATM 7 O O2B AGS . . . C 3 18.671 79.754 28.217 1 26.41 ? O2B AGS 2001 A 1 HETATM 8 O O3B AGS . . . C 3 19.157 78.401 30.266 1 31.69 ? O3B AGS 2001 A 1 HETATM 9 P PA AGS . . . C 3 17.376 76.289 27.393 1 24.37 ? PA AGS 2001 A 1 HETATM 10 O O1A AGS . . . C 3 17.533 76.531 25.954 1 29.54 ? O1A AGS 2001 A 1 HETATM 11 O O2A AGS . . . C 3 18.126 75.196 28.089 1 22.34 ? O2A AGS 2001 A 1 HETATM 12 O O3A AGS . . . C 3 17.658 77.639 28.31 1 24.62 ? O3A AGS 2001 A 1 HETATM 13 O O5' AGS . . . C 3 15.834 76.332 27.636 1 21.71 ? O5' AGS 2001 A 1 HETATM 14 C C5' AGS . . . C 3 15.425 75.941 28.871 1 24.62 ? C5' AGS 2001 A 1 HETATM 15 C C4' AGS . . . C 3 13.933 76.044 28.97 1 24.46 ? C4' AGS 2001 A 1 HETATM 16 O O4' AGS . . . C 3 13.342 75.21 28.042 1 23.97 ? O4' AGS 2001 A 1 HETATM 17 C C3' AGS . . . C 3 13.49 75.612 30.348 1 27.81 ? C3' AGS 2001 A 1 HETATM 18 O O3' AGS . . . C 3 12.792 76.646 31.029 1 28.27 ? O3' AGS 2001 A 1 HETATM 19 C C2' AGS . . . C 3 12.671 74.331 30.165 1 29.32 ? C2' AGS 2001 A 1 HETATM 20 O O2' AGS . . . C 3 11.341 74.373 30.77 1 36.66 ? O2' AGS 2001 A 1 HETATM 21 C C1' AGS . . . C 3 12.628 74.176 28.629 1 28.01 ? C1' AGS 2001 A 1 HETATM 22 N N9 AGS . . . C 3 13.145 72.857 28.132 1 27.6 ? N9 AGS 2001 A 1 HETATM 23 C C8 AGS . . . C 3 14.398 72.396 27.726 1 28.66 ? C8 AGS 2001 A 1 HETATM 24 N N7 AGS . . . C 3 14.525 71.13 27.326 1 28.41 ? N7 AGS 2001 A 1 HETATM 25 C C5 AGS . . . C 3 13.242 70.711 27.484 1 28.4 ? C5 AGS 2001 A 1 HETATM 26 C C6 AGS . . . C 3 12.581 69.448 27.269 1 29.94 ? C6 AGS 2001 A 1 HETATM 27 N N6 AGS . . . C 3 13.31 68.288 26.778 1 29.35 ? N6 AGS 2001 A 1 HETATM 28 N N1 AGS . . . C 3 11.224 69.336 27.53 1 30.55 ? N1 AGS 2001 A 1 HETATM 29 C C2 AGS . . . C 3 10.493 70.438 28.006 1 32.15 ? C2 AGS 2001 A 1 HETATM 30 N N3 AGS . . . C 3 10.995 71.686 28.255 1 28.36 ? N3 AGS 2001 A 1 HETATM 31 C C4 AGS . . . C 3 12.372 71.76 27.986 1 27.36 ? C4 AGS 2001 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #