data_1ION # _model_server_result.job_id wkQsDM_3XuohTFFMW4aPMQ _model_server_result.datetime_utc '2024-11-01 17:21:05' _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 1ion # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1ION # _exptl.entry_id 1ION _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1ION _cell.length_a 96.59 _cell.length_b 96.59 _cell.length_c 96.59 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ION _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N THR 2 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale2 A C GLU 29 A GLU 29 1_555 A N MSE 30 A MSE 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C MSE 30 A MSE 30 1_555 A N GLY 31 A GLY 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C THR 42 A THR 42 1_555 A N MSE 43 A MSE 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 A C MSE 43 A MSE 43 1_555 A N ALA 44 A ALA 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C TYR 74 A TYR 74 1_555 A N MSE 75 A MSE 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C MSE 75 A MSE 75 1_555 A N THR 76 A THR 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C ALA 127 A ALA 127 1_555 A N MSE 128 A MSE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 A C MSE 128 A MSE 128 1_555 A N SER 129 A SER 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C ALA 130 A ALA 130 1_555 A N MSE 131 A MSE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C MSE 131 A MSE 131 1_555 A N LEU 132 A LEU 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 A C THR 151 A THR 151 1_555 A N MSE 152 A MSE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 A C MSE 152 A MSE 152 1_555 A N LYS 153 A LYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 A C GLY 155 A GLY 155 1_555 A N MSE 156 A MSE 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C MSE 156 A MSE 156 1_555 A N VAL 157 A VAL 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale16 A C VAL 188 A VAL 188 1_555 A N MSE 189 A MSE 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 A C MSE 189 A MSE 189 1_555 A N ASP 190 A ASP 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OG1 THR 17 A THR 17 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc2 C O3B ADP . A ADP 301 1_555 B MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc3 B MG MG . A MG 302 1_555 D O HOH . A HOH 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc4 B MG MG . A MG 302 1_555 D O HOH . A HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc5 B MG MG . A MG 302 1_555 D O HOH . A HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1ION _atom_sites.fract_transf_matrix[1][1] 0.010353 _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] 0.010353 _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] 0.010353 _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 B 2 MG A 1 302 302 MG MG . C 3 ADP A 1 301 301 ADP ADP . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 412 412 HOH HOH . D 4 HOH A 13 413 413 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 415 HOH HOH . D 4 HOH A 16 416 416 HOH HOH . D 4 HOH A 17 417 417 HOH HOH . D 4 HOH A 18 418 418 HOH HOH . D 4 HOH A 19 419 419 HOH HOH . D 4 HOH A 20 420 420 HOH HOH . D 4 HOH A 21 421 421 HOH HOH . D 4 HOH A 22 422 422 HOH HOH . D 4 HOH A 23 423 423 HOH HOH . D 4 HOH A 24 424 424 HOH HOH . D 4 HOH A 25 425 425 HOH HOH . D 4 HOH A 26 426 426 HOH HOH . D 4 HOH A 27 427 427 HOH HOH . D 4 HOH A 28 428 428 HOH HOH . D 4 HOH A 29 429 429 HOH HOH . D 4 HOH A 30 430 430 HOH HOH . D 4 HOH A 31 431 431 HOH HOH . D 4 HOH A 32 432 432 HOH HOH . D 4 HOH A 33 433 433 HOH HOH . D 4 HOH A 34 434 434 HOH HOH . D 4 HOH A 35 435 435 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 PB ADP . . . C 3 -20.393 32.514 39.094 1 25.94 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . C 3 -21.227 32.894 37.897 1 31.16 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . C 3 -20.644 31.073 39.666 1 25.97 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . C 3 -18.884 32.737 38.854 1 23.96 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . C 3 -20.071 34.776 40.849 1 29.4 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . C 3 -19.319 35.414 39.723 1 32.64 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . C 3 -19.388 34.486 42.091 1 32.48 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . C 3 -20.789 33.423 40.276 1 28.59 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . C 3 -21.26 35.712 40.992 1 38.84 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . C 3 -22.22 35.481 41.939 1 31.73 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . C 3 -22.843 36.784 42.331 1 31.13 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . C 3 -23.419 36.424 43.612 1 31.78 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . C 3 -21.906 38.005 42.649 1 29.41 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . C 3 -22.707 39.21 42.55 1 34.99 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . C 3 -21.48 37.852 44.195 1 30.75 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . C 3 -21.308 39.112 44.879 1 32.86 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . C 3 -22.71 36.99 44.642 1 27.1 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . C 3 -22.451 36.057 45.774 1 29.47 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . C 3 -21.881 34.863 45.639 1 27.23 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . C 3 -21.712 34.267 46.745 1 30.18 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . C 3 -22.211 35.158 47.705 1 28.78 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . C 3 -22.352 35.122 49.142 1 30.19 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . C 3 -21.958 34.035 49.895 1 26.02 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . C 3 -22.913 36.217 49.766 1 29.18 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . C 3 -23.294 37.267 49.026 1 26.85 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . C 3 -23.192 37.38 47.682 1 26.01 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . C 3 -22.647 36.29 47.093 1 27.31 ? C4 ADP 301 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #