data_3EUK # _model_server_result.job_id CA6Hm1d_0qaKnQoz6cip1Q _model_server_result.datetime_utc '2025-01-15 06:56:59' _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 3euk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2001}' # _entry.id 3EUK # _exptl.entry_id 3EUK _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 4 _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 3EUK _cell.length_a 172.414 _cell.length_b 172.414 _cell.length_c 491.587 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EUK _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA pentameric 5 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,C,I,J,K,L 1 1 D,E,F,G,H,M,N,O,P 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 ? 4 I N N ? 4 L N N ? 4 M N N ? 4 O N N # _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 3EUK _atom_sites.fract_transf_matrix[1][1] 0.0058 _atom_sites.fract_transf_matrix[1][2] 0.003349 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006697 _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] 0.002034 _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 I 4 AGS A 1 2001 2001 AGS ATG . J 5 MG A 1 2011 2011 MG MG . K 5 MG A 1 2012 2012 MG MG . L 4 AGS C 1 2002 2002 AGS ATG . M 4 AGS F 1 2003 2003 AGS ATG . N 5 MG F 1 2013 2013 MG MG . O 4 AGS H 1 2004 2004 AGS ATG . P 5 MG H 1 2014 2014 MG MG . # 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 . . . I 4 -44.012 80.637 31.858 1 116.39 ? PG AGS 2001 A 1 HETATM 2 S S1G AGS . . . I 4 -44.231 80.457 33.634 1 115.42 ? S1G AGS 2001 A 1 HETATM 3 O O2G AGS . . . I 4 -43.014 79.591 31.44 1 115.54 ? O2G AGS 2001 A 1 HETATM 4 O O3G AGS . . . I 4 -45.258 80.636 31.092 1 115.96 ? O3G AGS 2001 A 1 HETATM 5 P PB AGS . . . I 4 -42.267 82.989 31.92 1 123.47 ? PB AGS 2001 A 1 HETATM 6 O O1B AGS . . . I 4 -40.975 82.426 31.458 1 123.51 ? O1B AGS 2001 A 1 HETATM 7 O O2B AGS . . . I 4 -42.422 83.157 33.381 1 123.67 ? O2B AGS 2001 A 1 HETATM 8 O O3B AGS . . . I 4 -43.483 82.097 31.401 1 120.07 ? O3B AGS 2001 A 1 HETATM 9 P PA AGS . . . I 4 -41.256 85.332 30.58 1 130.48 ? PA AGS 2001 A 1 HETATM 10 O O1A AGS . . . I 4 -41.158 84.621 29.27 1 131.54 ? O1A AGS 2001 A 1 HETATM 11 O O2A AGS . . . I 4 -40.067 85.659 31.363 1 130.36 ? O2A AGS 2001 A 1 HETATM 12 O O3A AGS . . . I 4 -42.348 84.451 31.452 1 126.74 ? O3A AGS 2001 A 1 HETATM 13 O O5' AGS . . . I 4 -42.111 86.675 30.54 1 134.39 ? O5' AGS 2001 A 1 HETATM 14 C C5' AGS . . . I 4 -43.455 86.703 30.11 1 140.79 ? C5' AGS 2001 A 1 HETATM 15 C C4' AGS . . . I 4 -43.914 88.173 30.209 1 144.53 ? C4' AGS 2001 A 1 HETATM 16 O O4' AGS . . . I 4 -43.124 88.972 29.378 1 147.38 ? O4' AGS 2001 A 1 HETATM 17 C C3' AGS . . . I 4 -45.373 88.411 29.789 1 145.84 ? C3' AGS 2001 A 1 HETATM 18 O O3' AGS . . . I 4 -46.143 88.815 30.914 1 144.84 ? O3' AGS 2001 A 1 HETATM 19 C C2' AGS . . . I 4 -45.341 89.479 28.69 1 147.69 ? C2' AGS 2001 A 1 HETATM 20 O O2' AGS . . . I 4 -46.101 90.687 28.971 1 148.47 ? O2' AGS 2001 A 1 HETATM 21 C C1' AGS . . . I 4 -43.848 89.757 28.499 1 149.78 ? C1' AGS 2001 A 1 HETATM 22 N N9 AGS . . . I 4 -43.409 89.464 27.101 1 153.38 ? N9 AGS 2001 A 1 HETATM 23 C C8 AGS . . . I 4 -42.899 88.321 26.477 1 154.63 ? C8 AGS 2001 A 1 HETATM 24 N N7 AGS . . . I 4 -42.584 88.376 25.181 1 156.41 ? N7 AGS 2001 A 1 HETATM 25 C C5 AGS . . . I 4 -42.925 89.677 24.913 1 156.56 ? C5 AGS 2001 A 1 HETATM 26 C C6 AGS . . . I 4 -42.859 90.499 23.728 1 157.01 ? C6 AGS 2001 A 1 HETATM 27 N N6 AGS . . . I 4 -42.375 89.954 22.465 1 156.96 ? N6 AGS 2001 A 1 HETATM 28 N N1 AGS . . . I 4 -43.288 91.828 23.786 1 157.04 ? N1 AGS 2001 A 1 HETATM 29 C C2 AGS . . . I 4 -43.759 92.387 24.98 1 156.84 ? C2 AGS 2001 A 1 HETATM 30 N N3 AGS . . . I 4 -43.867 91.726 26.174 1 156.39 ? N3 AGS 2001 A 1 HETATM 31 C C4 AGS . . . I 4 -43.421 90.377 26.088 1 155.61 ? C4 AGS 2001 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #