data_8AMD # _model_server_result.job_id geQoGtGMxRE0nMuogBdrkg _model_server_result.datetime_utc '2024-12-27 01:35:28' _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 8amd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":500}' # _entry.id 8AMD # _exptl.entry_id 8AMD _exptl.method 'ELECTRON MICROSCOPY' # _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 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 90 _cell.entry_id 8AMD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N 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 covale ? covale1 A CA SER 82 A SER 82 1_555 F O1B AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale2 A N GLY 84 A GLY 84 1_555 F O2A AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale3 A CD1 TYR 116 A TYR 116 1_555 F N6 AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A NZ LYS 257 A LYS 257 1_555 F O3' AGS . A AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale5 C CA SER 82 B SER 82 1_555 G O1B AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale6 C N GLY 84 B GLY 84 1_555 G O2A AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale7 C CD1 TYR 116 B TYR 116 1_555 G N6 AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 C NZ LYS 257 B LYS 257 1_555 G O3' AGS . B AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale9 D CA SER 82 F SER 82 1_555 H O1B AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale10 D N GLY 84 F GLY 84 1_555 H O2A AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale11 D CD1 TYR 116 F TYR 116 1_555 H N6 AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 D NZ LYS 257 F LYS 257 1_555 H O3' AGS . F AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale13 E CA SER 82 G SER 82 1_555 I O1B AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale14 E CA GLY 84 G GLY 84 1_555 I O2A AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale15 E CD1 TYR 116 G TYR 116 1_555 I N6 AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale16 E NZ LYS 257 G LYS 257 1_555 I O3' AGS . G AGS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? # _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 8AMD _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 F 3 AGS A 1 500 500 AGS AGS . G 3 AGS B 1 500 500 AGS AGS . H 3 AGS F 1 500 500 AGS AGS . I 3 AGS G 1 500 500 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 . . . I 3 126.021 90.254 79.884 1 118.5 ? PG AGS 500 G 1 HETATM 2 S S1G AGS . . . I 3 126.997 91.809 79.245 1 118.5 ? S1G AGS 500 G 1 HETATM 3 O O2G AGS . . . I 3 126.944 89.008 79.93 1 118.5 ? O2G AGS 500 G 1 HETATM 4 O O3G AGS . . . I 3 124.841 89.975 78.918 1 118.5 ? O3G AGS 500 G 1 HETATM 5 P PB AGS . . . I 3 124.571 89.438 82.004 1 118.5 ? PB AGS 500 G 1 HETATM 6 O O1B AGS . . . I 3 123.652 90.07 82.986 1 118.5 ? O1B AGS 500 G 1 HETATM 7 O O2B AGS . . . I 3 123.892 88.689 80.858 1 118.5 ? O2B AGS 500 G 1 HETATM 8 O O3B AGS . . . I 3 125.481 90.522 81.312 1 118.5 ? O3B AGS 500 G 1 HETATM 9 P PA AGS . . . I 3 125.532 86.91 82.06 1 118.5 ? PA AGS 500 G 1 HETATM 10 O O1A AGS . . . I 3 126.258 86.987 80.782 1 118.5 ? O1A AGS 500 G 1 HETATM 11 O O2A AGS . . . I 3 124.096 86.384 81.949 1 118.5 ? O2A AGS 500 G 1 HETATM 12 O O3A AGS . . . I 3 125.455 88.344 82.705 1 118.5 ? O3A AGS 500 G 1 HETATM 13 O O5' AGS . . . I 3 126.415 86.076 83.078 1 118.5 ? O5' AGS 500 G 1 HETATM 14 C C5' AGS . . . I 3 125.898 85.272 84.177 1 118.5 ? C5' AGS 500 G 1 HETATM 15 C C4' AGS . . . I 3 126.339 85.778 85.536 1 118.5 ? C4' AGS 500 G 1 HETATM 16 O O4' AGS . . . I 3 127.529 85.106 85.984 1 118.5 ? O4' AGS 500 G 1 HETATM 17 C C3' AGS . . . I 3 126.636 87.264 85.675 1 118.5 ? C3' AGS 500 G 1 HETATM 18 O O3' AGS . . . I 3 126.222 87.696 86.967 1 118.5 ? O3' AGS 500 G 1 HETATM 19 C C2' AGS . . . I 3 128.155 87.347 85.468 1 118.5 ? C2' AGS 500 G 1 HETATM 20 O O2' AGS . . . I 3 128.723 88.343 86.308 1 118.5 ? O2' AGS 500 G 1 HETATM 21 C C1' AGS . . . I 3 128.657 85.954 85.873 1 118.5 ? C1' AGS 500 G 1 HETATM 22 N N9 AGS . . . I 3 129.552 85.324 84.914 1 118.5 ? N9 AGS 500 G 1 HETATM 23 C C8 AGS . . . I 3 129.269 85.096 83.596 1 118.5 ? C8 AGS 500 G 1 HETATM 24 N N7 AGS . . . I 3 130.211 84.462 82.95 1 118.5 ? N7 AGS 500 G 1 HETATM 25 C C5 AGS . . . I 3 131.186 84.255 83.909 1 118.5 ? C5 AGS 500 G 1 HETATM 26 C C6 AGS . . . I 3 132.436 83.612 83.859 1 118.5 ? C6 AGS 500 G 1 HETATM 27 N N6 AGS . . . I 3 132.933 83.047 82.752 1 118.5 ? N6 AGS 500 G 1 HETATM 28 N N1 AGS . . . I 3 133.159 83.56 85 1 118.5 ? N1 AGS 500 G 1 HETATM 29 C C2 AGS . . . I 3 132.648 84.101 86.11 1 118.5 ? C2 AGS 500 G 1 HETATM 30 N N3 AGS . . . I 3 131.476 84.72 86.278 1 118.5 ? N3 AGS 500 G 1 HETATM 31 C C4 AGS . . . I 3 130.783 84.756 85.133 1 118.5 ? C4 AGS 500 G 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #