data_5OG1 # _model_server_result.job_id flxEL-OGA3L6BJup4ypecw _model_server_result.datetime_utc '2024-10-20 20:06:16' _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 5og1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":901}' # _entry.id 5OG1 # _exptl.entry_id 5OG1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M _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 ? _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 ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M 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 5OG1 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 2 AGS C 1 901 901 AGS AGS . H 2 AGS C 1 902 902 AGS AGS . I 2 AGS E 1 901 901 AGS AGS . J 2 AGS E 1 902 902 AGS AGS . K 2 AGS D 1 901 901 AGS AGS . L 2 AGS D 1 902 902 AGS AGS . M 2 AGS B 1 901 901 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 . . . K 2 171.999 206.667 164.68 1 0 ? PG AGS 901 D 1 HETATM 2 S S1G AGS . . . K 2 173.074 205.055 164.479 1 0 ? S1G AGS 901 D 1 HETATM 3 O O2G AGS . . . K 2 171.464 207.092 163.283 1 0 ? O2G AGS 901 D 1 HETATM 4 O O3G AGS . . . K 2 170.792 206.376 165.62 1 0 ? O3G AGS 901 D 1 HETATM 5 P PB AGS . . . K 2 173.917 208.547 164.384 1 0 ? PB AGS 901 D 1 HETATM 6 O O1B AGS . . . K 2 174.874 207.45 163.91 1 0 ? O1B AGS 901 D 1 HETATM 7 O O2B AGS . . . K 2 174.587 209.652 165.104 1 0 ? O2B AGS 901 D 1 HETATM 8 O O3B AGS . . . K 2 172.853 207.819 165.293 1 0 ? O3B AGS 901 D 1 HETATM 9 P PA AGS . . . K 2 172.149 210.248 163.169 1 0 ? PA AGS 901 D 1 HETATM 10 O O1A AGS . . . K 2 171.033 209.788 162.229 1 0 ? O1A AGS 901 D 1 HETATM 11 O O2A AGS . . . K 2 172.791 211.547 162.874 1 0 ? O2A AGS 901 D 1 HETATM 12 O O3A AGS . . . K 2 173.205 209.075 163.093 1 0 ? O3A AGS 901 D 1 HETATM 13 O O5' AGS . . . K 2 171.532 210.359 164.616 1 0 ? O5' AGS 901 D 1 HETATM 14 C C5' AGS . . . K 2 170.101 210.573 164.735 1 0 ? C5' AGS 901 D 1 HETATM 15 C C4' AGS . . . K 2 169.804 211.997 165.143 1 0 ? C4' AGS 901 D 1 HETATM 16 O O4' AGS . . . K 2 170.669 212.371 166.234 1 0 ? O4' AGS 901 D 1 HETATM 17 C C3' AGS . . . K 2 170.021 213.058 164.07 1 0 ? C3' AGS 901 D 1 HETATM 18 O O3' AGS . . . K 2 168.839 213.237 163.299 1 0 ? O3' AGS 901 D 1 HETATM 19 C C2' AGS . . . K 2 170.343 214.306 164.892 1 0 ? C2' AGS 901 D 1 HETATM 20 O O2' AGS . . . K 2 169.164 214.985 165.308 1 0 ? O2' AGS 901 D 1 HETATM 21 C C1' AGS . . . K 2 171.077 213.719 166.101 1 0 ? C1' AGS 901 D 1 HETATM 22 N N9 AGS . . . K 2 172.529 213.747 165.996 1 0 ? N9 AGS 901 D 1 HETATM 23 C C8 AGS . . . K 2 173.365 212.714 165.665 1 0 ? C8 AGS 901 D 1 HETATM 24 N N7 AGS . . . K 2 174.635 213.036 165.656 1 0 ? N7 AGS 901 D 1 HETATM 25 C C5 AGS . . . K 2 174.635 214.373 166.017 1 0 ? C5 AGS 901 D 1 HETATM 26 C C6 AGS . . . K 2 175.673 215.31 166.193 1 0 ? C6 AGS 901 D 1 HETATM 27 N N6 AGS . . . K 2 176.966 215.024 166.026 1 0 ? N6 AGS 901 D 1 HETATM 28 N N1 AGS . . . K 2 175.329 216.567 166.554 1 0 ? N1 AGS 901 D 1 HETATM 29 C C2 AGS . . . K 2 174.036 216.859 166.721 1 0 ? C2 AGS 901 D 1 HETATM 30 N N3 AGS . . . K 2 172.975 216.061 166.586 1 0 ? N3 AGS 901 D 1 HETATM 31 C C4 AGS . . . K 2 173.345 214.827 166.227 1 0 ? C4 AGS 901 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 100 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #